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Supporting data for the paper 'Small-scale capillary heterogeneity linked to rapid plume migration during CO2 storage' by S.J. Jackson and S. Krevor 2020

Samuel Jackson & Samuel Krevor
Herein lies the supporting data for the paper 'Small-scale capillary heterogeneity linked to rapid plume migration during CO2 storage'. We supply experimental, analytical and numerical simulation data used in the paper. The supplied zipped folders follow the same order as the main paper, with codes to reproduce each figure (and those in the supporting information PDF). There are also video files (in the 5_Field_scale_simulation zipped folder) showing the final CO2 plume evolution from the static...

Complex histories of gene flow and a mitochondrial capture event in a non-sister pair of bird

Ethan Gyllenhaal, Michael Andersen, Jenna McCullough, Xena Mapel, Tri Haryoko, Knud Jønsson & Leo Joseph
Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter,...

Data from: High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Sue V. Song, Sharon Downes, Tracey Parker, John G. Oakeshott & Charles Robin
Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of ‘selective sweeps’. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci...

Data from: Going with the flow: the role of ocean circulation in global marine ecosystems under a changing climate

Simon J. Van Gennip, Ekaterina E. Popova, Andrew Yool, Gretta T. Pecl, Alistair J. Hobday & Cascade J. B. Sorte
Ocean warming, acidification, deoxygenation and reduced productivity are widely considered to be the major stressors to ocean ecosystems induced by emissions of CO2. However, an overlooked stressor is the change in ocean circulation in response to climate change. Strong changes in the intensity and position of the western boundary currents have already been observed, and the consequences of such changes for ecosystems are beginning to emerge. In this study, we address climatically induced changes in...

Data from: Fire, fragmentation, and windstorms: a recipe for tropical forest degradation

Divino V. Silvério, Paulo M. Brando, Mercedes M.C. Bustamante, Francis E. Putz, Daniel Magnabosco Marra, Shaun R. Levick & Susan E. Trumbore
1. Widespread degradation of tropical forests is caused by a variety of disturbances that interact in ways that are not well understood. 2. To explore potential synergies between edge effects, fire and windstorm damage as causes of Amazonian forest degradation, we quantified vegetation responses to a 30-minute high-intensity windstorm that in 2012, swept through a large-scale fire experiment that borders an agricultural field. Our pre- and post-windstorm measurements include tree mortality rates and modes of...

Data from: A seascape genetic analysis of a stress-tolerant coral species along the Western Australian coast

Richard D. Evans, Nicole M. Ryan, Michael J. Travers, Ming Feng, Yvette Hitchen & W. Jason Kennington
Genetic diversity and connectivity are key factors in determining a population’s resilience to future disturbance. This is especially relevant to corals, which are in global decline due to increasing frequency and strength of thermal anomalies and severe tropical cyclones. While many studies have investigated genetic diversity and population structure in corals, they focused on species being removed at the greatest rate from coral reefs, Acroporids and Pocilloporids, and it is unclear whether the patterns observed...

Data from: Incorporating existing thermal tolerance into projections of compositional turnover under climate change

Alex Bush, Renee Catullo, Karel Mokany, Tom Harwood, Andrew Hoskins & Simon Ferrier
Aim: Observed, realized niche space often underestimates species’ physiological tolerances due to interactions with other species, dispersal constraints, and because some combinations of influential environmental factors do not currently exist in the real world. Conversely, correlative ecological niche models rely on the assumption that the range of environmental conditions encompassed by a species’ geographic distribution accurately reflects their environmental tolerances, including community-level approaches like Generalised Dissimilarity Modelling (GDM). We extend GDM to better understand what...

Data from: Reliable species distributions are obtainable with sparse, patchy and biased data by leveraging over species and data types

Samantha L. Peel, Nicole A. Hill, Scott D. Foster, Simon J. Wotherspoon, Claudio Ghiglione & Stefano Schiaparelli
1. New methods for species distribution models (SDMs) utilise presence‐absence (PA) data to correct the sampling bias of presence‐only (PO) data in a spatial point process setting. These have been shown to improve species estimates when both data sets are large and dense. However, is a PA data set that is smaller and patchier than hitherto examined able to do the same? Furthermore, when both data sets are relatively small, is there enough information contained...

Data from: Marine plastic pollution in waters around Australia: characteristics, concentrations, and pathways

Julia Reisser, Jeremy Shaw, Chris Wilcox, Britta Denise Hardesty, Maira Proietti, Michele Thums & Charitha Pattiaratchi
Plastics represent the vast majority of human-made debris present in the oceans. However, their characteristics, accumulation zones, and transport pathways are still poorly assessed. We characterised and estimated the concentration of marine plastics in waters around Australia using surface net tows, and inferred their potential pathways using particle-tracking models and real drifter trajectories. The 839 marine plastics recorded were predominantly small fragments (“microplastics”, median length = 2.8 mm, mean length = 4.9 mm) resulting from...

Data from: Introgression and the fate of domesticated genes in a wild mammal population

Philine G. D. Feulner, Jacob Gratten, James W. Kijas, Peter M. Visscher, Josephine M. Pemberton, Jon Slate & Jon. Slate
When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re-introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high-throughput genotyping with 25 years of long-term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free-living Soay sheep of St Kilda, and more modern...

Data from: Predicting local adaptation in fragmented plant populations: implications for restoration genetics

Melinda Pickup, David L. Field, David M. Rowell & Andrew G. Young
Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined if spatial scale (0.7 – 600km), environmental distance, quantitative Q_ST and neutral genetic differentiation F_ST, and size of the local and foreign populations could predict patterns of adaptive differentiation....

Data from: Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: genetic diversity and relationships from 1976 to 2007

Dieter M. Bulach, David B. Boyle, Rebecca A. Halpin, David J. Spiro, Laura W. Pomeroy & Daniel A. Janies
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...

Data from: Genome-wide transcriptional signatures of migratory flight activity in a globally invasive insect pest

Christopher M. Jones, Alexie Papanicolaou, George K. Mironidis, John Vontas, Yihua Yang, Ka S. Lim, Kumar S. Singh, John G. Oakeshott, Christopher Bass, Jason W. Chapman & Chris Bass
Migration is a key life history strategy for many animals and requires a suite of behavioural, morphological and physiological adaptations which together form the ‘migratory syndrome’. Genetic variation has been demonstrated for many traits that make up this syndrome, but the underlying genes involved remain elusive. Recent studies investigating migration-associated genes have focussed on sampling migratory and nonmigratory populations from different geographic locations but have seldom explored phenotypic variation in a migratory trait. Here, we...

Data from: Dynamic species co-occurrence networks require dynamic biodiversity surrogates

Ayesha I. T. Tulloch, Iadine Chadès, Yann Dujardin, Martin J. Westgate, Peter W. Lane & David Lindenmayer
In conservation it is inevitable that surrogates be selected to represent the occurrence of hard–to–find species and find priority locations for management. However, species co–occurrence can vary over time. Here we demonstrate how temporal dynamics in species co–occurrence influence the ability of managers to choose the best surrogate species. We develop an efficient optimisation formulation that selects the optimal set of complementary surrogate species from any co–occurrence network. We apply it to two Australian datasets...

Data from: Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

Austen C. Thomas, Bruce E. Deagle, J. Paige Eveson, Corie H. Harsch & Andrew W. Trites
DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field...

Data from: Genetic parameters in subtropical pine F1 hybrids: heritabilities, between-trait correlations and genotype-by-environment interactions

Washington J. Gapare, Pomerayi Mutete & Ruramai Murepa
Growth and stem straightness traits of 29 Pinus caribaea var. hondurensis × Pinus tecunumanii (PCH × PTEC) and 26 P. caribaea var. hondurensis × Pinus oocarpa (PCH × POOC) hybrid pair-crosses plus a total of 16 intraspecific families were assessed at ages 5, 8 and 15 years from planting at two sites. The PCH × PTEC hybrid was the most productive, yielding 37 % more than a Pinus elliottii local control and was 21 %...

Data from: Anthropogenic debris ingestion by avifauna in eastern Australia

Lauren Roman, Qamar A. Schuyler, Britta Denise Hardesty & Kathy A. Townsend
Anthropogenic debris in the world’s oceans and coastal environments is a pervasive global issue that has both direct and indirect impacts on avifauna. The number of bird species affected, the feeding ecologies associated with an increased risk of debris ingestion, and selectivity of ingested debris have yet to be investigated in most of Australia’s coastal and marine birds. With this study we aim to address the paucity of data regarding marine debris ingestion in Australian...

Data from: Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon

James W. Kijas, Nick Elliot, Peter Kube, Bradley Evans, Natasha Botwright, Harry King, Craig R. Primmer, Klara Verbyla & J. Kijas
Farmed Atlantic salmon (Salmo salar) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome-wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNPs in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage...

Data from: Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)

Gaynor Dolman & Leo Joseph
Background: During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today’s diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the...

Data from: Inferring contemporary and historical genetic connectivity from juveniles

Pierre Feutry, Oliver Berry, Peter M. Kyne, Richard D. Pillans, Rich Hillary, Peter M. Grewe, James R. Marthick, Grant Johnson, Rasanthi M. Gunasekera, Nicholas J. Bax, Mark Bravington & Richard M. Hillary
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark...

Data from: Local demographic and epidemiological patterns in the Linum marginale – Melampsora lini association – a multi-year study

Hanna Susi, Peter H. Thrall, Luke G. Barrett & Jeremy J. Burdon
1.Many theoretical and empirical studies operate from an assumption that pathogens have a significant influence on the fecundity and lifespan of their host species. However, there is surprisingly little data investigating the long-term fitness impacts and genetic consequences that arise from pathogen infection in natural populations. Here, we address this gap through the analysis of a dataset investigating the local population dynamics of a native host plant (Linum marginale) and an associated rust pathogen (Melampsora...

Data from: Genome-wide scans detect adaptation to aridity in a widespread forest tree species.

Dorothy A. Steane, Brad M. Potts, Elizabeth McLean, Suzanne M. Prober, William D. Stock, René E. Vaillancourt & Margaret Byrne
Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Burning for biodiversity: highly resilient ant communities respond only to strongly contrasting fire regimes in Australia’s seasonal tropics

Alan N. Andersen, Relena R. Ribbons, Magen Pettit & Catherine L. Parr
1. According to the pyrodiversity paradigm, a wide range of fire regimes is required to maintain biodiversity in fire-prone landscapes. However, the requisite level of pyrodiversity has seldom been tested and may actually be very low. 2. Here, we examine the sensitivity of tropical savanna ants to variation in fire regimes using results from a long-term fire experiment near Darwin, Australia. Six experimental fire regimes, with varying fire frequency and seasonality, have been applied to...

Data from: The ‘heritability’ of domestication and its functional partitioning in the pig

Miguel Perez-Enciso, Gustavo De Los Campos, Nick Hudson, James Kijas & Antonio Reverter
We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to...

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  • Commonwealth Scientific and Industrial Research Organisation
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