44 Works

Data from: Computational performance and statistical accuracy of *BEAST and comparisons with other methods

Huw A. Ogilvie, Joseph Heled, Dong Xie & Alexei J. Drummond
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation...

Data from: Why pair? Evidence of aggregative mating in a socially monogamous marine fish (Siganus doliatus, Siganidae)

Rebecca J. Fox, David R. Bellwood & Michael D. Jennions
Many species live in stable pairs, usually to breed and raise offspring together, but this cannot be assumed. Establishing whether pairing is based on mating, or an alternative cooperative advantage, can be difficult, especially where species show no obvious sexual dimorphism and where the act of reproduction itself is difficult to observe. In the tropical marine fishes known as rabbitfish (Siganidae), half of extant species live in socially monogamous, territorial pairs. It has been assumed...

Data from: Characterization of the placoderm (Gnathostomata) assemblage from the tetrapod-bearing locality of Strud (Belgium, Upper Famennian)

Sébastien Olive, Gaël Clément, Edward B. Daeschler & Vincent Dupret
The placoderm fauna of the late Famennian tetrapod-bearing locality of Strud, Belgium, is studied on the basis of historical and newly collected material. It includes the previously described antiarch Grossilepis rikiki, the groenlandaspidid Turrisaspis strudensis sp. nov. and the actinolepidoideid Phyllolepis undulata. P. undulata is thoroughly described and joins the list of the valid Phyllolepis species confidently diagnosed. A morphometrical analysis performed on the centronuchal and anterior ventrolateral plates of the Phyllolepis material demonstrates that...

Data from: Parental effects alter the adaptive value of an adult behavioural trait

Rebecca M. Kilner, Giuseppe Boncoraglio, Jono M. Henshaw, Benjamin J. M. Jarrett, Ornela De Gasperin, Hanna Kokko, Benjamin JM Jarrett, Alfredo Attisano & Jonathan M Henshaw
The parents' phenotype, or the environment they create for their young, can have long-lasting effects on their offspring, with profound evolutionary consequences. Yet virtually no work has considered how such parental effects might change the adaptive value of behavioural traits expressed by offspring upon reaching adulthood. To address this problem, we combined experiments on burying beetles (Nicrophorus vespilloides) with theoretical modelling, and focussed on one adult behavioural trait in particular: the supply of parental care....

Data from: Fine-scale refuges can buffer demographic and genetic processes against short-term climatic variation and disturbance: a 22 year case study of an arboreal marsupial

Sam C. Banks, Thibault Lorin, Robyn E. Shaw, Lachlan McBurney, David Blair, Michaela D. J. Blyton, Annabel L. Smith, Jennifer C. Pierson, David B. Lindenmayer & Michaela D.J. Blyton
Ecological disturbance and climate are key drivers of temporal dynamics in the demography and genetic diversity of natural populations. Microscale refuges are known to buffer species’ persistence against environmental change, but the effects of such refuges on demographic and genetic patterns in response to short-term environmental variation are poorly understood. We quantified demographic and genetic responses of mountain brushtail possums (Trichosurus cunninghami) to rainfall variability (1992–2013) and to a major wildfire. We hypothesized that there...

Data from: The effect of sex-biased dispersal on opposite-sexed spatial genetic structure and inbreeding risk

Michaela D. J. Blyton, Sam C. Banks & Rod Peakall
Natal sex-biased dispersal has long been thought to reduce the risk of inbreeding by spatially separating opposite-sexed kin. Yet, comprehensive and quantitative evaluations of this hypothesis are lacking. In this study, we quantified the effectiveness of sex-biased dispersal as an inbreeding avoidance strategy by combining spatially explicit simulations and empirical data. We quantified the extent of kin clustering by measuring the degree of spatial autocorrelation among opposite-sexed individuals (FM structure). This allowed us to systematically...

Data from: An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation

Peter E. Smouse, Michael R. Whitehead & Rod Peakall
Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require ‘common currency’ translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi-parentally inherited diploid nuclear markers, and then extend...

Data from: Assessing the alignment of sexual and natural selection using radio-mutagenized seed beetles

Daniel J. Power & Luke Holman
A major unsolved question in evolutionary biology concerns the relationship between natural and sexual selection. Sexual selection might augment natural selection, e.g. if mutations that harm female fecundity also reduce male mating success. Conversely, sexual selection might favor traits that impair naturally-selected fitness components. We induced detrimental mutations in Callosobruchus maculatus beetles using X-ray irradiation, and then experimentally measured the effect of pre-copulatory sexual selection on offspring number and survival rate. Sexual selection treatment had...

Data from: Tackling extremes: challenges for ecological and evolutionary research on extreme climatic events

Liam D. Bailey & Martijn Van De Pol
1. Extreme climatic events (ECEs) are predicted to become more frequent as the climate changes. A rapidly increasing number of studies - though few on animals - suggest that the biological consequences of ECEs can be severe. 2. However, ecological research on the impacts of extreme climatic events (ECEs) has been limited by a lack of cohesiveness and structure. ECEs are often poorly defined and have often been confusingly equated with climatic variability, making comparison...

Data from: Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations, and introgression between winged and wingless forms

Nicolas Dussex, Aaron Chuah & Jonathan M. Waters
Insect flight-loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in co-distributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain...

Data from: Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns

Timothy Linksvayer, Alexander Mikheyev, Timothy A Linksvayer & Alexander S Mikheyev
MySQL database for gene expression analysisMySQL database for the transcriptional, network connectedness, molecular evolution, and GO term analysismonomorium_2014-12-08.sql.gzData tables from MySQL database for gene expression analysisseparated data tables from MySQL database as zipped .csv files for the transcriptional, network connectedness, molecular evolution, and GO term analysismonomorium tables.zipdata summary by genesummary of data listed by M. pharaonis gene in comma deliminated (.csv) format. Header line with variables: gene is the M. pharaonis gene name; SINV homolog...

Data from: The extent and consequences of p-hacking in science

Megan L. Head, Luke Holman, Rob Lanfear, Andrew T. Kahn & Michael D. Jennions
A focus on novel, confirmatory, and statistically significant results leads to substantial bias in the scientific literature. One type of bias, known as “p-hacking,” occurs when researchers collect or select data or statistical analyses until nonsignificant results become significant. Here, we use text-mining to demonstrate that p-hacking is widespread throughout science. We then illustrate how one can test for p-hacking when performing a meta-analysis and show that, while p-hacking is probably common, its effect seems...

Data from: Exon capture phylogenomics: efficacy across scales of divergence

Jason G. Bragg, Sally Potter, Ke Bi & Craig Moritz
The evolutionary histories of species are not measured directly, but estimated using genealogies inferred for particular loci. Individual loci can have discordant histories, but in general we expect to infer evolutionary histories more accurately as more of the genome is sampled. High Throughput Sequencing (HTS) is now providing opportunities to incorporate thousands of loci in ‘phylogenomic’ studies. Here, we used target enrichment to sequence c.3000 protein-coding exons in a group of Australian skink lizards (crown...

Data from: Mismatch in the distribution of floral ecotypes and pollinators: insights into the evolution of sexually deceptive orchids

Ryan D. Phillips, Bjorn Bohman, Janet M. Anthony, Siegfried L. Krauss, Kingsley W. Dixon & Rod Peakall
Plants are predicted to show floral adaptation to geographic variation in the most effective pollinator, potentially leading to reproductive isolation and genetic divergence. Many sexually deceptive orchids attract just a single pollinator species, limiting opportunities to experimentally investigate pollinator switching. Here we investigate Drakaea concolor, which attracts two pollinator species. Using pollinator choice tests, we detected two morphologically similar ecotypes within D. concolor. The common ecotype only attracted Zaspilothynnus gilesi, while the rare ecotype also...

Data from: Prolific observer bias in the life sciences: why we need blind data recording

Luke Holman, Megan L. Head, Robert Lanfear & Michael D. Jennions
Observer bias and other “experimenter effects” occur when researchers’ expectations influence study outcome. These biases are strongest when researchers expect a particular result, are measuring subjective variables, and have an incentive to produce data that confirm predictions. To minimize bias, it is good practice to work “blind,” meaning that experimenters are unaware of the identity or treatment group of their subjects while conducting research. Here, using text mining and a literature review, we find evidence...

Data from: Bet hedging via multiple mating: a meta-analysis

Luke Holman
Polyandry has been hypothesized to allow females to “bet hedge” against mating only with unsuitable mates, reducing variance in offspring fitness between members of a polyandrous lineage relative to a single-mating one. Theoretically, this reduction in fitness variance could select for polyandrous genotypes even when polyandry carries a direct cost, especially in small populations. However, this hypothesis is controversial and difficult to test empirically. Here, I apply a novel simulation model to 49 published empirical...

Data from: Evidence for inbreeding depression in a species with limited opportunity for maternal effects

Regina Vega-Trejo, Megan L. Head & Michael D. Jennions
It is often assumed that mating with close relatives reduces offspring fitness. In such cases, reduced offspring fitness may arise from inbreeding depression (i.e., genetic effects of elevated homozygosity) or from post-mating maternal investment. This can be due to a reduction in female investment after mating with genetically incompatible males (“differential allocation”) or compensation for incompatibility (“reproductive compensation”). Here, we looked at the effects of mating with relatives on offspring fitness in mosquitofish, Gambusia holbrooki....

Data from: Coevolution is linked with phenotypic diversification but not speciation in avian brood parasites

Iliana Medina & Naomi E. Langmore
Coevolution is often invoked as an engine of biological diversity. Avian brood parasites and their hosts provide one of the best-known examples of coevolution. Brood parasites lay their eggs in the nests of other species, selecting for host defences and reciprocal counter-adaptations in parasites. In theory, this arms race should promote increased rates of speciation and phenotypic evolution. Here we use recently developed methods to test whether the three largest avian brood parasitic lineages show...

Data from: Salt tolerance is evolutionarily labile in a diverse set of angiosperm families

Camile Moray, Xia Hua & Lindell Bromham
Background: Salt tolerance in plants is rare, yet they it is found across a diverse set of taxonomic groups. This suggests that, although salt tolerance involves a complex set of traits, it has evolved many times independently in different angiosperm lineages. However, the pattern of evolution of salt tolerance can vary dramatically between families. A recent phylogenetic study of the Chenopodiaceae (goosefoot family) concluded that salt tolerance has a conserved evolutionary pattern, being gained early...

Data from: Proximate mechanisms of colour variation in the frillneck lizard: geographical differences in pigment contents of an ornament

Thomas Merkling, David G. Hamilton, Borbala Cser, Nina Svedin & Sarah R. Pryke
Animal coloration has evolved in contexts such as communication, camouflage, and thermoregulation. Most studies of animal coloration focus on its adaptive benefits, whereas its underlying mechanisms have received less attention despite their potential influence on adaptive benefits. In fish and reptiles, for example, colour variation from yellow to red can be produced by carotenoid and/or pteridine pigments, which differ dramatically in the way they are obtained (carotenoids through diet and pteridines synthesized de novo). Hence,...

Data from: Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Craig Moritz, Matthew Fujita, Dan F. Rosauer, Rosa Agudo, Gayleen Bourke, Russell Palmer, Mitzy Pepper, Sally Potter, Renae Pratt, Mitchell Scott, Maria Tonione, Stephen Donnellan, Paul Doughty, D. Rosauer & M. K. Fujita
Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics includes vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Though recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock-restricted taxa. To provide a baseline for ongoing comparative analyses, we...

Data from: A rigorous comparison of sexual selection indexes via simulations of diverse mating systems

Jonathan M. Henshaw, Andrew T. Kahn & Karoline Fritzsche
Sexual selection is a cornerstone of evolutionary theory, but measuring it has proved surprisingly difficult and controversial. Various proxy measures—e.g., the Bateman gradient and the opportunity for sexual selection—are widely used in empirical studies. However, we do not know how reliably these measures predict the strength of sexual selection across natural systems, and most perform poorly in theoretical worst-case scenarios. Here we provide a rigorous comparison of eight commonly used indexes of sexual selection. We...

Data from: Dynamics of pre-choice and post-choice behaviour: rats approximate optimal strategy in a discrete-trial decision task

Justine Fam, Reginald Fred Westbrook, Ehsan Arabzadeh & F. Westbrook
We simulate two types of environments to investigate how closely rats approximate optimal foraging. Rats initiated a trial where they chose between two spouts for sucrose, which was delivered at distinct probabilities. The discrete trial procedure used allowed us to observe the relationship between choice proportions, response latencies and obtained rewards. Our results show that rats approximate the optimal strategy across a range of environments that differ in the average probability of reward as well...

Data from: Genetic distance for a general non-stationary Markov substitution process

Benjamin D. Kaehler, Von Bing Yap, Rongli Zhang & Gavin A. Huttley
The genetic distance between biological sequences is a fundamental quantity in molecular evolution. It pertains to questions of rates of evolution, existence of a molecular clock, and phylogenetic inference. Under the class of continuous-time substitution models, the distance is commonly defined as the expected number of substitutions at any site in the sequence. We eschew the almost ubiquitous assumptions of evolution under stationarity and time-reversible conditions and extend the concept of the expected number of...

Data from: Groundwater salinisation intensifies drought impacts in forests and reduces refuge capacity

Jarrod Kath, Sue Powell, Kathryn Reardon-Smith, Sondoss El Sawah, Anthony J. Jakeman, Barry F. W. Croke & Fiona J. Dyer
1. Shallow groundwater aquifers regularly support drought refuges for water-dependent ecosystems. However, many aquifers are impacted by over-extraction and pollution, potentially degrading their ability to support groundwater-fed drought refuges. 2. We investigated the response of groundwater-connected riverine forests to a drought considered equivalent in intensity to those predicted under severe climate change for 2030. The drought's impact was investigated in an area where shallow groundwater resources are heavily exploited and polluted by salinization. 3. We...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Australian National University
  • James Cook University
  • University of Cambridge
  • Macquarie University
  • Commonwealth Scientific and Industrial Research Organisation
  • University of Exeter
  • University of Helsinki
  • University of Canberra
  • NSW Office of Environment & Heritage
  • Max Planck Institute for Dynamics and Self Organization