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Data from: The search for loci under selection: trends, biases and progress
No full textDetecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAA) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analyzed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographic coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.<br><br><h3>Usage Notes</h3><br>Table S1 - Full data set.Data was collected by reading papers associated with environmental association analyses. Data includes location, species, methods used, genetic parameters of data sets reviewed, and analytical parameters of the analyses.Table S1_data.xlsxR code for mixed-effects linear modelsThe R code used to create the figures and estimate regressions of the data set.Ahrens et al 2018_MolEcol_review.
Data from: To recycle or steal? Nutrient resorption in Australian and Brazilian mistletoes from three low-phosphorus sites
No full textResorption is the process by which nutrients are withdrawn from leaves prior to leaf fall. Mistletoes are generally thought not to rely on nutrient resorption; being xylem-tapping parasites, they instead derive the nutrients required for new growth from their host plant, at little or no cost. We measured nutrient (N, P, K, Ca, Mg) resorption in 18 parasitic mistletoe–host species pairs distributed across three sites with notably low-P soil, also quantifying relationships with leaf lifespan (LL) and specific leaf area (SLA). There was little or no evidence of N, Ca or Mg resorption. By contrast, on average ∼30% of P and ∼20% of K were resorbed prior to leaf fall. Longer LL in mistletoes was associated with lower N and P concentrations in mistletoes and in host leaves. We provide evidence that, even though mistletoes are relatively inefficient in terms of nutrient resorption compared to non-parasite species, on low-P soils their ecological and evolutionary strategies for conserving phosphorous involve modulation of both leaf lifespan and P concentration in senesced leaves.<br><br><h3>Usage Notes</h3><br>Data_Scalon et al. OikosValues of specific leaf area (SLA), and leaf nitrogen, phosphorus, potassium, magnesium and calcium concentrations for mistletoes and host species. Green leaf nutrient concentration are shown for mistletoes ([Nut]_green) and hosts ([Nut]_host). Senescent leaf nutrient concentration are shown for mistletoes only ([Nut]_old)
Data from: Water quality assessment of Australian ports using water quality evaluation indices
No full textAustralian ports serve diverse and extensive activities, such as shipping, tourism and fisheries, which may all impact the quality of port water. In this work water quality monitoring at different ports using a range of water quality evaluation indices was applied to assess the port water quality. Seawater samples at 30 stations in the year 2016–2017 from six ports in NSW, Australia, namely Port Jackson, Botany, Kembla, Newcastle, Yamba and Eden, were investigated to determine the physicochemical and biological variables that affect the port water quality. The large datasets obtained were designed to determine the Water Quality Index, Heavy metal Evaluation Index, Contamination Index and newly developed Environmental Water Quality Index. The study revealed medium water quality index and high and medium heavy metal evaluation index at three of the study ports and high contamination index in almost all study ports. Low level dissolved oxygen and higher level of total dissolved solids, turbidity, fecal coliforms, copper, iron, lead, zinc, manganese, cadmium and cobalt are mainly responsible for the poor water qualities of the port areas. Good water quality at the background samples indicated that various port activities are the likely cause for poor water quality inside the port area.<br><br><h3>Usage Notes</h3><br>S1 Table Sample site identificationTable S1 Table.: Sample site identification.S2 Table Standards for Marine water ecosystemS2 Table.: Australian and international standards and guidelines for marine water ecosystem.S3 Table Original data for water quality parametersS3 Table.: Original data for water quality parameters.S4 Table EWQI calculationS4 Table.: Calculation data for Environmental Water Quality Index (EWQI)
Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone
No full textThe exploration of hybrid zones and the intergenomic conflicts exposed through hybridization provide windows into the processes of divergence and speciation. Sex chromosomes and mitonuclear incompatibilities have strong associations with the genetics of hybrid dysfunction. In ZW sex-determining systems, maternal co-inheritance of the mitochondrial and W chromosomes immediately exposes incompatibilities between these maternal contributions of one species and the Z chromosome of another. We analyze mitochondrial and Z chromosome admixture in the long-tailed finch (Poephila acuticauda) of Australia, where hybridizing subspecies differ prominently in Z chromosome genotype and in bill color, yet the respective centers of geographic admixture for these two traits are offset by 350 km. We report two well-defined mitochondrial clades that diverged ~0.5 Mya. Mitochondrial contact is geographically co-located within a hybrid zone of Z chromosome admixture and is displaced from bill color admixture by nearly 400 km. Consistent with Haldane’s rule expectations, hybrid zone females are significantly less likely than males to carry an admixed Z chromosome or have mismatched Z-mitochondrial genotypes. Furthermore, there are significantly fewer than expected mitonuclear mismatches in hybrid zone females and paternal backcross males. Results suggest a potential for mitonuclear/sex chromosome incompatibilities in the emergence of reproductive isolation in this system
Mimicry in motion and morphology: do information limitation, trade-offs or compensation relax selection for mimetic accuracy?
No full textMany animals mimic dangerous or undesirable prey as a defence from predators. We would expect predators to reliably and exclusively avoid animals that closely resemble dangerous prey, yet imperfect mimics are common. There have been many hypotheses suggested to explain imperfect mimicry, but comparative tests across multiple mimicry systems are needed to determine which are applicable, and which—if any—represent general principles of imperfect mimicry. We tested four hypotheses on Australian ant mimics and found support for only one of them: the information limitation hypothesis. A predator with incomplete information will be unable to discriminate some poor mimics from their models. We also show that since predators must make decisions while they are learning, they are likely to never sample broadly enough to gain and utilise the full information needed to discriminate poor mimics from their models. We found no evidence that one accurate mimetic trait can compensate for another, or that rapid movement reduces selection pressure for good mimicry. Based on our results, we argue that information limitation is likely to be a general principle behind imperfect mimicry of any complex traits, while interactions between components of mimicry may apply to some mimicry systems but not others.<br><br><br><h3>Methods</h3><br>This data set is a zip file containing both data and code (R scripts). Data include videos of walking arthropods, from which trajectories are extracted, and outlines derived from still photographs, which are used to analyse body shape. The R scripts are used to process and analyse the data. The data set contains README.md and README.txt files that describe the structure of the data set in more detail.<br><br><br><h3>Usage Notes</h3><br>The data set contains README.md and README.txt files that describe the data set
Rates of attraction of cane toad tadpoles to chemicals
No full textChemical cues produced by late-stage embryos of the cane toad (Rhinella marina) attract older conspecific larvae, which are highly cannibalistic and can consume an entire clutch. To clarify the molecular basis of this attraction response, we presented captive tadpoles with components present in toad eggs. As previously reported, attractivity arises from the distinctive toxins (bufadienolides) produced by cane toads, with some toxins (e.g., bufagenins) much stronger attractants than others (e.g., bufotoxins). Extracts of frozen toad parotoid glands (rich in bufagenins) were more attractive than were fresh MeOH extracts of the parotoid secretion (rich in bufotoxins), and purified marinobufagin was more effective than marinobufotoxin. Cardenolide aglycones (e.g., digitoxigenin) were active attractors, whereas C-3 glycosides (e.g., digoxin, oubain) were far less effective. A structure-activity relationship study revealed that tadpole attractant potency strongly correlated with Na+/K+ ATPase inhibitory activity, suggesting that tadpoles monitor and rapidly react to perturbations to Na+/K+ ATPase activity
Sea snake approaches to divers
No full textScuba-divers on tropical coral-reefs often report unprovoked “attacks” by highly venomous Olive sea snakes (Aipysurus laevis). Snakes swim directly towards divers, sometimes wrapping coils around the diver’s limbs and biting. Based on a focal animal observation study of free-ranging Olive sea snakes in the southern Great Barrier Reef, we suggest that these “attacks” are misdirected courtship responses. Approaches to divers were most common during the breeding season (winter) and were by males rather than by female snakes. Males also made repeated approaches, spent more time with the diver, and exhibited behaviours (such as coiling around a limb) also seen during courtship. Agitated rapid approaches by males, easily interpreted as “attacks”, often occurred after a courting male lost contact with a female he was pursuing, after interactions between rival males, or when a diver tried to flee from a male. These patterns suggest that “attacks” by sea snakes on humans result from mistaken identity during sexual interactions. Rapid approaches by females occurred when they were being chased by males. Divers that flee from snakes may inadvertently mimic the responses of female snakes to courtship, encouraging males to give chase. To prevent escalation of encounters, divers should keep still and avoid retaliation.<br><br><br><h3>Methods</h3><br>A diver recorded interactions with free-ranging snakes
The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest
No full textBiogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure show patterns that are associated with environmental variables also known to predict the density of A. femoralis.<br><br><br><h3>Methods</h3><br>Extraction of DNA and single-nucleotide polymorphism (SNP) discovery was carried out at Diversity Arrays Technology sequencing Pty. Ltd. (DArTseq) facility (Canberra, Australia; more detail, please see the Supplementary Information in the article). A modified double-digest restriction-site associated DNA sequencing protocol was performed on libraries prepared using a combination of Pstl-Hpall restriction enzymes. The Pstl enzyme adaptor also contained an Illumina adaptor sequence, a primer sequence and a variable-length barcode. The Hpall adaptor contained an Illumina flow cell attachment and overhang sequence. Following enzymatic digestion, fragments were amplified and sequenced on an Illumina HiSeq2500. DNA sequences were aligned via BLAST using the Nanorana parkeri reference genome. To check for contamination, sequences were also blasted to bacterial and fungal genomes (NCBI).<br><br><br><h3>Usage Notes</h3><br>This data set was filtered for missing data using the filter_dart function of the R package RADIATOR v. 0.010. Only individuals and loci with ≥95% SNPs geno- typed were retained. SNPs were also screened for allele coverage, with any SNPs displaying a local and global minor allele frequency threshold of less than 1% removed from the dataset. In cases where multiple SNPs were found within the same read, only one locus was retained (chosen randomly per RAD tag) to avoid statistical bias from physical linkage. Two samples from M14 had <95% of loci genotyped and were removed, which resulted in 64 individuals from 13 populations genotyped at 10 275 SNPs (please see the article Table S2 for summary of filtering steps)
Datasets related to Key Trends and Drivers in Military Modernization in the Indo-Pacific: Implications for Australia and Responses
No full text<p>This dataset underlies the report generated entitled "Key Trends and Drivers in Military Modernization in the Indo-Pacific: Implications for Australia and Responses" by Bates Gill, Yves-Heng Lim, Antoine Levesques, Adam Lockyer, Fred Smith, Rahul Roy-Chaudhury, Viraj Solanki and Andrew T. H. Tan. </p><br><p>This project addresses the priority Defence policy topic of Accelerating Regional Military Modernization (and Asymmetric Advantages). It assesses the trends, attributes and drivers of accelerating military modernization in the Indo-Pacific, in order to understand and clearly delineate the challenges facing Australia. The report then proceeds to examine the roles of the key actors in this phenomenon, namely, China, the United States and India. Finally, the project puts forward and assesses potential Australian responses in the face of the region’s accelerating military modernization dynamic.</p><br><p><br></p><br><p>The dataset is made up of the following:</p><br><p>1. Estimated_Personnel_in_the_PRC_Armed_Forces_2016_and_2020.csv</p><br><p>2. Selected_PLA_Weaponry_2020.csv </p><br><p>3. Report - Military Modernization in the Indo-Pacific.pdf </p><br><p>4. Seminar_Recording_1920x1080_GMT20220915-020051.mp4</p>
Raw Data and STATA data file for the Manuscript titled Adverse Childhood Experiences and Obsessive-Compulsive Personality Traits: Effects of Attachment, Intolerance of Uncertainty, and Metacognition
No full text<p dir="ltr">This study aimed to investigate whether attachment-anxiety, intolerance of uncertainty, and metacognition have indirect effects in the association between ACEs and Obsessive-Compulsive Personality Traits (OCPT) in various network models. Undergraduate psychology students (N = 291) participated in an anonymous 30-minute online survey consisting of a series of self-report questionnaires regarding adverse childhood experiences, attachment, intolerance of uncertainty, metacognition, OCPT, and depression. Bootstrapped serial mediation revealed attachment-anxiety and intolerance of uncertainty had a serial-mediation effect in the association between ACEs and OCPT. Serial mediation was not found for metacognition and attachment-anxiety. However, metacognition alone mediated between child emotional abuse and OCPT. These findings expand our currently limited knowledge regarding the etiology of OCPT and suggest that attachment-anxiety, intolerance of uncertainty, and metacognition may be important contributors for understanding the development of OCPT following ACE exposure.</p><p dir="ltr">This item contains the raw data and the STATA dta. file for this project.</p>