35 Works

Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris Sea Urchins

Phillip Davidson, Haobing Guo, Abdull Massri, Jane Swart, Allison Edgar, Haobing Guo, Hannah Devens, Alejandro Berrio, Lingyu Wang, Demian Koop, Paula Cisternas, He Zhang, Yaloei Zhang, Maria Byrne, Guangyi Fan & Gregory Wray
Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on interactions with these networks remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyze genomes, epigenomes, and transcriptomes during early development in two sea urchin species in the...

Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins

Phillip Davidson, Maria Byrne & Greg Wray
Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin configuration to the evolution of gene expression and organismal traits. Genome-wide assays of chromatin configuration, coupled with whole-genome alignments, can help address this gap in knowledge in several ways. In this study, we present a comparative analysis of regulatory element sequences and...

Country interaction matrix for territorial footprints

Amanda Irwin

Data for Rates of warming impact oxidative stress in zebrafish (Danio rerio)

Frank Seebacher, Isabella Loughland, Giggi Y. Lau & Jordan Jolly
Potentially negative effects of thermal variation on physiological functions may be modulated by compensatory responses, but their efficacy depends on the timescale of phenotypic adjustment relative to the rate of temperature change. Increasing temperatures in particular can affect mitochondrial bioenergetics and rates of reactive oxygen species (ROS) production. Our aim was to test whether different rates of temperature increase impact mitochondrial bioenergetics and modulate oxidative stress. We exposed zebrafish (Danio rerio) to warming from 20...

Country specific extinction-risk footprint details

Amanda Irwin

Endocrine disruption from plastic pollution and warming interact to increase the energetic cost of growth in a fish

Frank Seebacher, Nicholas Wu & Rubin Alexander
Energetic cost of growth determines how much food-derived energy is needed to produce a given amount of new biomass, and thereby influences energy transduction between trophic levels. Growth and development are regulated by hormones and are therefore sensitive to changes in temperature and environmental endocrine disruption. Here we show that the endocrine disruptor bisphenol A at an environmentally relevant concentration (BPA; 10 µg l⁻¹) decreased fish (Danio rerio) size at 30 oC water temperature. Under...

Phylogenetic analysis of policistronic amino-acid sequences encoded by 116 flavivirus genomes

Lars Jermiin, Vivek Jayaswal & John Robinson
Recently, Genome Biology and Evolution (11:3341-3352) published three statistical tests for testing whether alignments of sequence data violate the phylogenetic assumption of evolution under homogeneous conditions. The tests extend the matched-pairs tests of symmetry, marginal symmetry, and internal symmetry for pairs of aligned homologous sequences to the case where a whole alignment is considered. Here we reveal that the new tests are misleading. We explain why this is so, reveal how the tests of whole...

Patch quality and habitat fragmentation shape the foraging patterns of a specialist folivore

Mathew Crowther, Adrian Rus, Valentina Mella, Mark Krockenberger, Jasmine Lindsay, Ben Moore & Clare McArthur
Research on use of foraging patches has focused on why herbivores visit or quit patches, yet little is known about visits to patches over time. Food quality, as reflected by higher nutritional quality and lower plant defences, and physical patch characteristics, which offer protection from predators and weather, affect patch use and hence should influence their revisitation. Due to the potentially high costs of moving between patches, fragmented habitats are predicted to complicate foraging decisions...

Transcript- and annotation-guided genome assembly of the European starling

Katarina Stuart, Richard Edwards, Yuanyuan Cheng, Wes Warren, Dave Burt, William Sherwin, Natalie Hofmeister, Scott Werner, Gregory Ball, Melissa Bateson, Matthew Brandley, Katherine Buchanan, Phillip Cassey, David Clayton, Tim De Meyer, Simone Meddle & Lee Rollins
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length...

Bait uptake by scavengers in tropical waterbodies

Richard Shine, Abhilasha Aiyer, Tina Bell, Ruchira Somaweera, Miles Bruny & Georgia Ward-Fear
In tropical Australia, conditioned taste aversion can buffer vulnerable native predators from the invasion of a toxic prey species (cane toads, Rhinella marina). Thus, we need to develop methods to deploy aversion-inducing baits in the field, in ways that maximize uptake by vulnerable species (but not other taxa). We constructed and field-tested baiting devices, in situ with wild animals. Apparatus were set next to waterbodies and baited concurrently at multiple locations (over water, water’s edge...

Registration Year

  • 2022

Resource Types

  • Dataset


  • University of Sydney
  • University of Queensland
  • Macquarie University
  • The University of Sydney
  • Sun Yat-sen University
  • Shanghai University
  • University of Alabama at Birmingham
  • Jiangsu Second Normal University
  • Huazhong University of Science and Technology
  • Duke University