ORCID Profile
0000-0003-0385-5939
Current Organisations
Manchester Metropolitan University
,
Michigan State University
,
BiomeBank
,
University of Manchester
,
University of Leeds
,
University of Exeter
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Publications
Evolutionary rates for multivariate traits: the role of selection and genetic variation
Publisher: Cold Spring Harbor Laboratory
Date: 14-02-2014
DOI: 10.1101/002683
Abstract: A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation ( Δz = Gβ ), which predicts evolutionary change for a suite of phenotypic traits ( Δz ) as a product of directional selection acting on them ( β ) and the genetic variance-covariance matrix for those traits ( G ). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are in part due to genetic architecture. We find evidence that sexually selected traits exhibit faster rates of evolution compared to life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.
Pair fidelity in long-lived parrots: genetic and behavioural evidence from the Crimson Rosella (Platycercus elegans)
Publisher: Informa UK Limited
Date: 02-04-2018
Spectral sensitivity of cone photoreceptors and opsin expression in two colour-divergent lineages of the lizard Ctenophorus decresii
Publisher: The Company of Biologists
Date: 09-2015
DOI: 10.1242/JEB.131854
Longevity, calling effort, and metabolic rate in two populations of cricket
Publisher: Springer Science and Business Media LLC
Date: 15-04-2011
ALTITUDINAL CLINAL VARIATION IN WING SIZE AND SHAPE IN AFRICANDROSOPHILA MELANOGASTER: ONE CLINE OR MANY?
Publisher: Wiley
Date: 07-09-2012
Incursions of Candida auris into Australia, 2018
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 06-2020
An Integrative Framework for the Appraisal of Coloration in Nature
Publisher: University of Chicago Press
Date: 06-2015
DOI: 10.1086/681021
Abstract: The world in color presents a dazzling dimension of phenotypic variation. Biological interest in this variation has burgeoned, due to both increased means for quantifying spectral information and heightened appreciation for how animals view the world differently than humans. Effective study of color traits is challenged by how to best quantify visual perception in nonhuman species. This requires consideration of at least visual physiology but ultimately also the neural processes underlying perception. Our knowledge of color perception is founded largely on the principles gained from human psychophysics that have proven generalizable based on comparative studies in select animal models. Appreciation of these principles, their empirical foundation, and the reasonable limits to their applicability is crucial to reaching informed conclusions in color research. In this article, we seek a common intellectual basis for the study of color in nature. We first discuss the key perceptual principles, namely, retinal photoreception, sensory channels, opponent processing, color constancy, and receptor noise. We then draw on this basis to inform an analytical framework driven by the research question in relation to identifiable viewers and visual tasks of interest. Consideration of the limits to perceptual inference guides two primary decisions: first, whether a sensory-based approach is necessary and justified and, second, whether the visual task refers to perceptual distance or discriminability. We outline informed approaches in each situation and discuss key challenges for future progress, focusing particularly on how animals perceive color. Given that animal behavior serves as both the basic unit of psychophysics and the ultimate driver of color ecology/evolution, behavioral data are critical to reconciling knowledge across the schools of color research.
Salmonella enterica Serovar Hvittingfoss in Bar-Tailed Godwits (Limosa lapponica) from Roebuck Bay, Northwestern Australia
Publisher: American Society for Microbiology
Date: 17-09-2020
DOI: 10.1128/AEM.01312-20
Abstract: Salmonella is a zoonotic pathogen that causes gastroenteritis and other disease presentations in both humans and animals. Serovars of S. enterica commonly cause foodborne disease in Australia and globally. In 2016-2017, S . Hvittingfoss was responsible for an outbreak that resulted in 110 clinically confirmed human cases throughout Australia. The origin of the contamination that led to the outbreak was never definitively established. Here, we identify a migratory shorebird, the bar-tailed godwit, as an animal reservoir of S . Hvittingfoss. These birds were s led in northwestern Australia during their nonbreeding period. The presence of a genetically similar S . Hvittingfoss strain circulating in a wild bird population, 2 years after the 2016-2017 outbreak and ∼1,500 km from the suspected source of the outbreak, demonstrates a potentially unidentified environmental reservoir of S . Hvittingfoss. While the birds cannot be implicated in the outbreak that occurred 2 years prior, this study does demonstrate the potential role for wild birds in the transmission of this important foodborne pathogen.
Complete microbial genomes for public health in Australia and the Southwest Pacific
Publisher: Microbiology Society
Date: 12-2020
Abstract: Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.
Parent-embryo acoustic communication: a specialised heat vocalisation allowing embryonic eavesdropping
Publisher: Springer Science and Business Media LLC
Date: 07-12-2018
DOI: 10.1038/S41598-018-35853-Y
Abstract: Sound is arguably the external cue most accessible to embryos of many species, and as such may constitute an unrivalled source of early information. Recent evidence shows that prenatal sounds, similarly to maternal effects, may shape developmental trajectories. Establishing whether parental vocalisations are signals directed at embryos, or parental cues on which embryos eavesdrop, can elucidate whether parents or embryos control developmental outcomes. Prenatal exposure to a characteristic heat-related parental call was recently shown to alter zebra finch growth and fitness. Here, we test the ecological context of this behaviour in the wild, and assess the information value and specificity of this vocalisation for an embryonic audience. We show that wild zebra finches also produce this characteristic call, only at high temperatures. In addition, in the lab, we demonstrate experimentally that calling is specifically triggered by high air temperatures, can occur without an embryonic audience, and importantly, is predicted by in iduals’ body mass. Overall, our findings reveal a specialised heat vocalisation that enables embryonic eavesdropping, by indicating high ambient temperatures, and parents’ capacity to cope with such conditions. This challenges the traditional view of embryos as passive agents of their development, and opens exciting research avenues on avian adaptation to extreme heat.
Complete microbial genomes for public health in Australia and Southwest Pacific
Publisher: Cold Spring Harbor Laboratory
Date: 05-11-2019
DOI: 10.1101/829663
Abstract: Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs. Whole-genome sequence (WGS) data is increasingly important in public health microbiology (1–4). The data can be used to replicate many of the basic bacterial sub-typing approaches, as well as support epidemiological investigations, such as surveillance and outbreak investigation (5–7). The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens that can provide easily portable data that promotes deeper integration of surveillance and investigation efforts across jurisdictions. This promise is leading to a concerted effort to move microbial public health to a primarily genome-based workflow at numerous jurisdictions (8–10), including Australia (11).
Heavy rainfall triggers increased nocturnal flight in desert populations of the Pacific black duck (Anas superciliosa)
Publisher: Springer Science and Business Media LLC
Date: 14-12-2017
DOI: 10.1038/S41598-017-17859-0
Abstract: Understanding of avian nocturnal flight comes mainly from northern hemisphere species in seasonal temperate ecosystems where nocturnal flight is often precisely timed and entrained by annual photoperiod. Here we investigate patterns of nocturnal flight in waterbirds of Australian desert ecosystems that fly considerable distances to find temporary water bodies formed from rainfall which is highly unpredictable seasonally and spatially, and when there is sufficient water, they then breed. How they perform these feats of navigation and physiology remain poorly known. Using GPS tracking of 38 satellite tagged Pacific black ducks ( Anas superciliosa ) in two contrasting ecosystems, before and after heavy rainfall we revealed a key role for facultative nocturnal flight in the movement ecology of this species. After large rainfall events, birds rapidly increased nocturnal flight activity in the arid aseasonal ecosystem, but not in the mesic seasonal one. Nocturnal flights occurred throughout the night in both ecosystems. Long range flights ( km in 2 hours) occurred almost exclusively at night at night the distance flown was higher than during the day, birds visited more locations, and the locations were more widely dispersed. Our work reveals that heavy rainfall triggers increased nocturnal flight activity in desert populations of waterbirds.
Multistate Outbreak of Salmonella enterica Serovar Heidelberg with Unidentifi ed Source, Australia, 2018-2019
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 2022
The power of a multivariate approach to genome-wide association studies: an example with Drosophila melanogaster wing shape
Publisher: Cold Spring Harbor Laboratory
Date: 14-02-2017
DOI: 10.1101/108308
Abstract: Due to the complexity of genotype-phenotype relationships, simultaneous analyses of genomic associations with multiple traits will be more powerful and more informative than a series of univariate analyses. In most cases, however, studies of genotype-phenotype relationships have analyzed only one trait at a time, even as the rapid advances in molecular tools have expanded our view of the genotype to include whole genomes. Here, we report the results of a fully integrated multivariate genome-wide association analysis of the shape of the Drosophila melanogaster wing in the Drosophila Genetic Reference Panel. Genotypic effects on wing shape were highly correlated between two different labs. We found 2,396 significant SNPs using a 5% FDR cutoff in the multivariate analyses, but just 4 significant SNPs in univariate analyses of scores on the first 20 principal component axes. A key advantage of multivariate analysis is that the direction of the estimated phenotypic effect is much more informative than a univariate one. Exploiting this feature, we show that the directions of effects were on average replicable in an unrelated panel of inbred lines. Effects of knockdowns of genes implicated in the initial screen were on average more similar than expected under a null model. Association studies that take a phenomic approach in considering many traits simultaneously are an important complement to the power of genomics. Multivariate analyses of such data are more powerful, more informative, and allow the unbiased study of pleiotropy.
Spectral sensitivity of cone photoreceptors and opsin expression in two colour-divergent lineages of the lizardCtenophorus decresii
Publisher: The Company of Biologists
Date: 2015
DOI: 10.1242/JEB.119404
Abstract: Intraspecific differences in sensory perception are rarely reported but may occur when a species range extends across varying sensory environments, or there is coevolution between the sensory system and a varying signal. Ex les in colour vision and colour signals are rare in terrestrial systems. The tawny dragon lizard Ctenophorus decresii is a promising candidate for such intraspecific variation, because the species comprises two geographically and genetically distinct lineages in which throat colour (a social signal used in intra- and inter-specific interactions) is locally adapted to the habitat and differs between lineages. Male lizards from the southern lineage have UV-blue throats, whereas males from the northern lineage are polymorphic with four discrete throat colours that all show minimal UV reflectance. Here we determine the cone photoreceptor spectral sensitivities and opsin expression of the two lineages, to test whether they differ, particularly in the UV wavelengths. Using microspectrophotometry on retinal cone photoreceptors, we identified a long wavelength sensitive visual pigment, a ‘short’ and ‘long’ medium wavelength sensitive pigment and a short wavelength sensitive pigment, all of which did not differ in λmax between lineages. Through transcriptome analysis of opsin genes we found that both lineages express four cone opsin genes, including that SWS1 opsin with peak sensitivity in the UV range, and that amino acid sequences did not differ between lineages with the exception of a single leucine/valine substitution in the RH2 opsin. Counts of yellow and transparent oil droplets associated with LWS+MWS and SWS+UVS cones respectively showed no difference in relative cone proportions between lineages. Therefore, contrary to predictions, we find no evidence of differences between lineages in single cone photoreceptor spectral sensitivity or opsin expression however, we confirm the presence of four single cones classes and thus likely tetrachromacy in C. decresii, and provide the first evidence of UV sensitivity in agamid lizards.
How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects
Publisher: Public Library of Science (PLoS)
Date: 22-11-2017
An image database of Drosophila melanogaster wings for phenomic and biometric analysis
Publisher: Oxford University Press (OUP)
Date: 22-05-2015
Adaptation to a novel predator inDrosophila melanogaster: How well are we able to predict evolutionary responses?
Publisher: Cold Spring Harbor Laboratory
Date: 19-05-2014
DOI: 10.1101/005322
Abstract: Evolutionary theory is sufficiently well developed to allow for short-term prediction of evolutionary trajectories. In addition to the presence of heritable variation, prediction requires knowledge of the form of natural selection on relevant traits. While many studies estimate the form of natural selection, few examine the degree to which traits evolve in the predicted direction. In this study we examine the form of natural selection imposed by mantid predation on wing size and shape in the fruitfly, Drosophila melanogaster . We then evolve populations of D. melanogaster under predation pressure, and examine the extent to which wing size and shape have responded in the predicted direction. We demonstrate that wing form partially evolves along the predicted vector from selection, more so than for control lineages. Furthermore, we re-examined phenotypic selection after ~30 generations of experimental evolution. We observed that the magnitude of selection on wing size and shape was diminished in populations evolving with mantid predators, while the direction of the selection vector differed from that of the ancestral population for shape. We discuss these findings in the context of the predictability of evolutionary responses, and the need for fully multivariate approaches.
Long incubation bouts and biparental incubation in the nomadic Banded Stilt
Publisher: Informa UK Limited
Date: 03-2016
DOI: 10.1071/MU15061
How predator hunting-modes affect prey behaviour: Capture deterrence in Drosophila melanogaster
Publisher: Cold Spring Harbor Laboratory
Date: 14-10-2014
DOI: 10.1101/010330
Abstract: Hunting mode or the distinct set of behavioural strategies that a predator employs while hunting can be an important determinant of the prey organism?s behavioural response. However, few studies have considered the predator?s hunting mode while describing differences in anti-predatory behaviours of a prey species. Here we document the influence of active hunters (zebra jumping spiders, Salticus scenicus ) and ambush predators (Chinese praying mantids, Tenodera aridifolia sinensis ) on the capture deterrence anti-predatory behavioural repertoire of the model organism, Drosophila melanogaster . We hypothesized that D. melanogaster would reduce overall locomotory activity in the presence of ambush predators, and increase them with active hunters. First we observed and described the behavioural repertoire of D. melanogaster in the presence of the predators. We documented three previously undescribed behaviours- abdominal lifting, stopping and retreat- which were performed at higher frequency by D. melanogaster in the presence of predators, and may aid in capture deterrence. Consistent with our predictions, we observed an increase in the overall activity of D. melanogaster in the presence of jumping spiders (active hunter). However, counter to our prediction, mantids (ambush hunter) had only a modest influence on activity. Given these new insights into Drosophila behaviour, and with the genetic tools available, dissecting the molecular mechanisms of anti-predator behaviours may now be feasible in this system.
Transcriptome Analysis Indicates Considerable Divergence in Alternative Splicing Between Duplicated Genes in Arabidopsis thaliana
Publisher: Oxford University Press (OUP)
Date: 16-10-2014
DOI: 10.1534/GENETICS.114.169466
Abstract: Gene and genome duplication events have created a large number of new genes in plants that can erge by evolving new expression profiles and functions (neofunctionalization) or iding extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or downregulation of gene expression by transcript decay. Using RNA-seq, we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in α-whole-genome duplicates and 33% of AS events in tandem duplicates are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this ergence. Conserved events had different frequencies, as only 31% of shared AS events in α-whole-genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative ergence. Analysis of published RNA-seq data from nonsense-mediated decay (NMD) mutants indicated that 85% of α-whole-genome duplicates and 89% of tandem duplicates have erged in their AS-induced NMD. Our results indicate that alternative splicing shows a high degree of ergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative ergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level ergence.
Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild caught populations ofDrosophila melanogaster<
Publisher: Cold Spring Harbor Laboratory
Date: 12-05-2022
DOI: 10.1101/2022.05.12.491649
Abstract: Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies (GWAS) have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to s ling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a GWAS (Pitchers et al. 2019) in three genes: dachsous (ds) , extra-macrochaete (emc) and neuralized (neur), using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the ds shape change vector, we observe genetic differentiation of variants in ds and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the emc shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of ds , suggesting that the available genetic ersity of a population, summarized by the genetic (co)variance matrix ( G ), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.
Limited plasticity in the phenotypic variance‐covariance matrix for male advertisement calls in the black field cricket, Teleogryllus commodus
Publisher: Wiley
Date: 27-03-2013
DOI: 10.1111/JEB.12120
Proximate cues to phases of movement in a highly dispersive waterfowl, Anas superciliosa
Publisher: Springer Science and Business Media LLC
Date: 09-2015
Draft Genome Sequences of Four Citrobacter Isolates Recovered from Wild Australian Shorebirds
Publisher: American Society for Microbiology
Date: 07-01-2021
DOI: 10.1128/MRA.01113-20
Abstract: Citrobacter is a ubiquitous bacterial genus whose members inhabit a variety of niches. Some species are clinically important for both antimicrobial resistance (AMR) carriage and as the cause of nosocomial infections. Surveillance of Citrobacter species in the environment can provide indicators of the spread of AMR genes outside clinical spaces. In this study, we present draft genome sequences of four Citrobacter isolates obtained from three species of wild Australian shorebirds.
Electric fish genomics: Progress, prospects, and new tools for neuroethology
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.JPHYSPARIS.2016.10.003
Abstract: Electric fish have served as a model system in biology since the 18th century, providing deep insight into the nature of bioelectrogenesis, the molecular structure of the synapse, and brain circuitry underlying complex behavior. Neuroethologists have collected extensive phenotypic data that span biological levels of analysis from molecules to ecosystems. This phenotypic data, together with genomic resources obtained over the past decades, have motivated new and exciting hypotheses that position the weakly electric fish model to address fundamental 21
Intraspecific geographic variation in rod and cone visual pigment sensitivity of a parrot, Platycercus elegans
Publisher: Springer Science and Business Media LLC
Date: 27-01-2017
DOI: 10.1038/SREP41445
Abstract: Variation in wavelength sensitivity among subspecies is unknown among vertebrates. The parrot Platycercus elegans has extreme plumage variation between subspecies ranging from pale yellow to crimson which, with differences in background colour and light environment between subspecies, makes it a good candidate for the evolution of within-species differences in vision. We report differences in visual pigments between populations of P. elegans from two subspecies, providing the first known support for population and subspecies variation in visual pigments within a vertebrate species it is also the first instance of intraspecific variation in rod sensitivity within any vertebrate species. Differences in wavelength sensitivity of rods and cones corresponded to geographic differences in plumage colour. Between study populations, visual pigments varied but not oil droplets. Adaptive functions for the visual pigment differences are untested but they could cause ergence in behaviours associated with colour as well as in dim light, and provide insights into the role of senses in ergence and speciation.
Related Organisations
Manchester Metropolitan University
Location: United Kingdom of Great Britain and Northern Ireland
University Of Manchester
Location: United Kingdom of Great Britain and Northern Ireland
University Of Leeds
Location: United Kingdom of Great Britain and Northern Ireland
University Of Exeter
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
No related grants have been discovered for William Pitchers.