Dogs are uniquely associated with human dispersal and bring novel insight into human migration and the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. The exact origin(s) and people(s) who transported the canines that became dingoes to Australia is debated, but it has been suggested they arrived by boat ~5,000-8,000 BP. Published morphological and genetic evidence has established the presence of at least two dingo lineages. The Alpine dingo is commonly found in south-eastern Australia while the Desert ecotype is found in the north, central and western Australia. The relationship of dingoes to modern dogs, and the ecotypes to each other, has important implications management and protection of this top predator, as well as providing interesting perspectives on human colonisation and canine domestication.
We have generated chromosome-level assemblies of both dingo ecotypes, along with domesticated dogs representing both ancient (Basenji) and derived (German Shepherd) breeds. In each case, long-read sequencing and Hi-C scaffolding have been combined to produce genome assemblies with high contiguity and structural completeness. Comparison of these assemblies with additional dog breeds, using the Greenland wolf as an outgroup, places the dingo as an early offshoot of modern dogs, situated between the grey wolf and the domesticated dogs of today. This is supported by patterns of genetic variation, and chromosome structure. Furthermore, we confirm that dingoes have not experienced the expansion of the AMY2B pancreatic amylase gene that occurred during domestication of modern dogs. This has important implications for dingo ecology and behaviour, and raises the prospect of using AMY2B copy number as a novel and reliable in-field discriminator between dingoes and feral dogs.
Thursday, 21 September 2023
PAG Australia 2023: Exploring Dingo Ecology and Evolution with Chromosome-Level Canid Genomes
Wednesday, 29 March 2023
The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology
Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V & Aiden EL (2023): The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 12:giad018. [Gigascience] [PubMed]
Background
One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.
Findings
We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog.
Conclusions
These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
Friday, 21 October 2022
The Ocean Genomes Lab is hiring - Bioinformatics and Sequencing technicians wanted!
Adding to the recently advertised Sequencing technician posts (closing 27 October), we are now pleased to advertise two bioinformatics research assistant positions to support our creation of marine vertebrate reference genome library. If you have experience with genome assembly or bioinformatics workflows, and are passionate about saving marine biodiversity, come and join us!
Two positions are available at Level 5 or 6, depending on your experience. Both roles will be providing bioinformatics support for our marine vertebrate reference genome project. You’ll get to play with data from the latest sequencing toys, including Illumina NovaSeq 6000, NextSeq 2000 and iSeq 100, the PacBio Sequel IIe, and ONT (probably PromethION and MinION).
Job roles will include developing and applying genome assembly workflows, data curation and QC, data sharing, and development/benchmarking of comparative genomics and genome assembly curation tools. If you have experience or passion for integrating bioinformatics workflows with Laboratory Information Management Systems and/or Electronic Laboratory Notebooks, we’d also love to hear to from you. SQL database skills would not go amiss too.
We’re a new team with lots to do, so there is plenty of scope to make the position your own and play to your strengths.
The closing date for applications is 11:55 PM AWST on Thursday 10 November 2022.
To learn more about these opportunities, please click here or contact Rich Edwards at rich.edwards@uwa.edu.au.
ABOUT THE TEAM
The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and Computational Biology Services.
Equipped with the latest high-throughput sequencing technology and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high quality marine vertebrate reference genome assemblies. All such reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly with open access.
The Ocean Genomes Laboratory will undertake research and development under the direction of Minderoo’s ambitious OceanOmics Program which has the goal of revolutionising ocean conservation through novel marine sampling and genomics approaches and scaling these to significantly advance our knowledge of marine life. The Ocean Genomes Laboratory and Computational Biology Services will include state of the art infrastructure including sample and eDNA preparation areas, flow cytometry, single cell sequencing equipment and the latest bioinformatics and computational biology tools.
Monday, 8 August 2022
Senior Postdoc wanted for UWA Ocean Genomes Lab! (Closing soon)
The new Ocean Genomes Laboratory (part of the Minderoo OceanOmics Centre at the UWA Oceans Institute) is hiring a Level B postdoc in marine genomics. (Three-year fixed term full time role, or flexible working equivalent.)
This is a rare opportunity to work as part of a collaborative team in a high-profile state of the art genomics research facility dedicated to studying marine vertebrates. You should have a PhD in bioinformatics, computational biology, molecular genetics or genomics, plus an interest in marine vertebrates and postdoctoral experience in high throughput DNA sequencing and whole genome assembly. The lab is new and there is plenty of scope to shape its direction beyond the core mission creating a marine vertebrate reference genome library as part of the Vertebrate Genome Project. You will also have an important role in helping to supervise the lab staff and research team.
Closing date: 11:55pm AWST, Friday 12 August 2022
Please see the UWA job advert for more details.
About the team
The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and a Computational Biology Program.
Equipped with the latest high-throughput sequencing technology, and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high-quality marine vertebrate reference genome assemblies. All reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly through open access.
The OceanOmics Centre will be located in the Bayliss Building on the UWA Crawley Campus, OceanOmics staff sharing the building with research and teaching staff primarily from the UWA School of Molecular Sciences and interacting with staff in the UWA Oceans Institute in the nearby IOMRC building.
About the opportunity
As a Research Fellow you will join a research group committed to applying modern molecular biological methods to marine research.
Using modern genomic approaches, you will undertake research on marine vertebrates, focussed on the production, QC and assembly of high-quality reference genome data. You will participate in the entire workflow from sample collection and processing, generating genomic sequence data in the laboratory using multiple modern genome sequencing technologies, with a focus on data processing, assembly, curation, analysis and dissemination.
In this unique role you will also be supported to develop your leadership skills. Working closely with the Centre’s UWA Principal Research Fellow, junior postdoctoral academics, the Centre’s Laboratory Manager, and diverse researchers from Minderoo Foundation you will contribute to decision making, oversee the work of technicians and PhD students and provide leadership in modern high-quality genome assembly production and publication.