ProfessorJaime Gongora

Project Opportunities

Title: Investigating the recent genomic demographic history in the platypus

Summary of opportunity:

This project investigates recent genomic demographic changes in the platypus (Ornithorhynchus anatinus), an iconic Australian species undergoing population decline due to habitat loss, fragmentation and river regulation, by integrating historical (50–200 years old) and contemporary whole-genome data. It aims to assess genetic diversity and demographic shifts in the last 500 years, including since European colonisation, identifying genetic erosion, bottlenecks, and changes in neutral and adaptive loci across river basin populations.

Opportunity synopsis:

This PhD project examines the recent demographic and genomic history of the platypus. While previous research has provided detailed insights into long-term demographic patterns and effective population size over deep evolutionary timescales (up to ~1 million years), far less is known about genetic changes over recent timescales, particularly across the past five centuries and since European colonisation approximately 200 years ago.

The project addresses this critical knowledge gap by integrating whole-genome data from ~80 contemporary platypuses (already generated) with genomic data from ~100 historical museum specimens, some of which are currently being generated. Using short-read shotgun sequencing and optimised ancient DNA protocols, the study will produce temporally stratified genomic datasets spanning the last 50–200 years.

Key aims include assessing changes in both neutral and adaptive genetic diversity, reconstructing evolutionary relationships through time, and inferring recent demographic trends such as population bottlenecks, fragmentation and potential recovery. Analytical approaches will apply coalescent modelling including GONG and PSMC framework to detect in effective population size, heterozygosity and allelic diversity.

This project will also involve laboratory-based DNA extraction, preparation of samples for whole-genome sequencing, and the development of skills in bioinformatic analyses and software for genome data processing and downstream analysis. By linking historical and contemporary genomic data, the project will generate high-resolution insights into genetic erosion and population dynamics across river basins, directly informing conservation strategies.

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Project Opportunities

Title: Unveiling the genomic basis of diversity and adaptation in the platypus

Summary of opportunity:

This project investigates the diversity of platypus genomes from across Australia and the impact of river regulation on adaptative loci. This project will involve bioinformatic analyses of genome data. 

Opportunity synopsis:

This project will focus on the diversity and selection of adaptive genes important for energy balance, metabolism, reproduction and immune response using genomes from platypuses from across Australia. It also assesses the impact of dams on gene flow between platypus populations. This project will involve bioinformatic analyses of genome data. 

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Project Opportunities

Title: Investigating the genomic diversity of the adaptive and innate immune systems in wild pigs and peccaries

Summary of opportunity:

This project focuses on elucidating the genetic diversity and differentiation of the adaptive and innate immune systems in wild pigs (Suidae) and peccaries (Tayassuidae) 

Opportunity synopsis:

This project will focus on the genetic diversity of different components of the immune system including he major histocompatibility complex and complement system across wild pig species from Africa, Europe and Asia and peccaries from the Americas. This project aims to improve our understanding of the mechanisms of evolution that have been shaping the diversity of wild pigs and peccaries in the last 35 million years. There is also the scope within this project to investigate MHC disease association including local adaptation of some of these species to some pathogens. This project will involved analyses of next generation sequencing data already available and validation using latest and traditional molecular genetic approaches.

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Project Opportunities

Title: Diversity of the immune system and conservation of the Arabian oryx

Summary of opportunity:

This project focuses on investigating the adaptive and immune systems of Arabian oryx from a reintroduction program in Oman. 

Opportunity synopsis:

This project investigates the genetic diversity of the adaptive and innate immune systems, including the major histocompatibility complex and complement system, in Arabian oryx breeding populations to better inform a reintroduction program for this species in Oman. There is also scope for investigating health parameters in these populations. This project will involve use of molecular genetic approaches and phylogenetic and population genetic analyses of DNA data.

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Project Opportunities

Title: Phylogenomics and diversification of peccaries from the Americas

Summary of opportunity:

This project focuses on the phylogenomic relationships of peccary species from the Americas 

Opportunity synopsis:

This project investigates the evolutionary relationships between the living peccary species from the Americas and assesses whether there has been undetected speciation occurring across the range of this family using genomic and phylogenetic approaches. There is also the scope within this project to investigate population structure and dispersal in some of these species using genotyping by sequencing (DaRT/RADseq). This project will involve use of next generation sequencing, phylogenetic and population genetic approaches.  

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Project Opportunities

Title: Population dispersal and genetic diversity of Australian crocodiles

Summary of opportunity:

This project focuses on investigating the population structure and dispersal of freshwater and saltwater crocodiles using genetic and genomic tools.

Opportunity synopsis:

This project investigates the level of genetic differentiation and gene flow within freshwater and saltwater crocodiles from northern Australia. This project will involve genotyping by sequencing (DaRT/RADseq) a large number of individuals/populations and estimating genetic population parameters. These datasets will be used as a framework to track the origins of unknown animals.

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Project Opportunities

Title: Peace with Nature: capacity building to document and protect biodiversity and promote sustainable green bioeconomy initiatives

Summary of opportunity:

Colombia is one of the most biodiverse country on Earth. However, protecting and undertaking research on this natural treasure has been extraordinarily difficult during Colombia’s lengthy civil war. The peace agreement between the former FARC-EP guerrilla and the Colombian government in 2016 opened access to key eco-regions. While this facilitated an advance in documenting biodiversity, it also led to increased biodiversity threats and loss. Since 2016, deforestation increased >65% across the country and >150% in protected areas. To address some of these complex issues, A/Prof Gongora established ‘Peace with Nature’, which focuses on empowering former guerrilla fighters, victims of the conflict and local communities to contribute to the protection of biodiversity, create new life choices and promote nature-based socioeconomic development in the Colombian Amazon. Peace with nature has created a unique model of training that includes participatory documentation (citizen science) of biodiversity and the co-design of nature-based activities to be incorporated into ecotourism projects established by excombatants. 

Opportunity synopsis:

This project focuses on evaluating the effectiveness of the capacity building approach and impact of Peace with Nature in documenting and protecting biodiversity and developing the green bioeconomy of local communities. This project will include three components: Implementation of surveys to obtain feedback from participants of the Peace with Nature project about knowledge and skills gained from workshops and practical activities; analyses of the benefits of learnt skills and knowledge in the generation of products and/or actions to be incorporated as part of the ecotourism offerings and in protection of biodiversity; and development, implementation and evaluation of citizen strategies to engage local communities and tourists in documenting and monitoring local biodiversity.

----------Current Research Projects----------

_x000D_ Conservation genomics of platypuses and oryxes

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_x000D_ Genetic traits of beauty, racing and milk camels

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_x000D_ Genomics of crocodilians

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_x000D_ Genetic diversity and evolution of adaptive and innate immune systems in wild pigs, peccaries, alligators and crocodiles

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_x000D_ Taxonomy and molecular systematics of peccaries and wild pigs

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_x000D_ Biodiversity conservation in the Amazon