Training Modules

Welcome to the Threatened Species Initiative (TSI) open online course: Conservation Genomics for Threatened Species Management. The training modules are presented by a range of Australian conservation geneticists who have generously given their time to assist us in improving genetic literacy and the use of genetic data in conservation management actions.

We hope you enjoy the modules!

These videos have been made available with the assistance of Australian BioCommons.

Our Stars – Find all our presenters in one place: The Presenters Page

Introduction – Threatened Species Initiative

This video provides a short introduction to the TSI, its objectives and why we have developed this online training course and what we hope to achieve.

Presenter: Carolyn Hogg

Module 1 – Principles of Population Genetics

During this module we will explore genetic terms and concepts that are essential for conservation managers to understand. The different videos will provide introductions to genetic markers, genetic diversity, population bottlenecks, reduced gene flow and genetic uniqueness.

1.1 Genetic markers

1.2 What is genomics/genetics?

1.3 Genetic bottlenecks and reduced gene flow

1.4 Restoring gene flow

1.5 Genetic uniqueness

Module 2 Introduction to Conservation Genetics and Management

This module explores how conservation genetics can inform management decisions and what conservation questions can be answered. We look at the role of conservation genetics in adaptive management frameworks and how the information can be used to inform conservation tools such as translocations and captive breeding.

2.1 Conservation genetics and why it matters to conservation management?

2.2 Decision support and risk assessment

2.3 Conservation genomics in action – animals

2.4 Conservation genomics in action – plants

Module 3 Recovery Teams, Conservation Agencies and Community Engagement

The three videos in this module focus on the importance of collaboration between researchers and managers, how to establish networks and different permitting considerations. We look at species-wide programs such as the NSW Saving Our Species program and Restore & Renew.

3.1 Co-design and engagement

3.2 Recovery teams and permitting

3.3 Species-wide genetics and biodiversity assessments

Module 4 Sample Collection, Storage and Study Design

Videos in this module explore the importance and function of reference genomes and population genetics for vertebrate, invertebrate and plant conservation projects. We look at different sampling methods for genetic material including non-invasive samples, low quality samples and eDNA.

4.1 Reference genomes and population genetics – vertebrates

4.2 Reference genomes and population genetics – invertebrates

4.3 Reference genomes and population genetics – plants

4.4 Non-invasive samples and low-quality samples

4.5 eDNA

4.6 Sampling design for breeding programs/seed banks/biobanks

Module 5 Overview of Conservation Genetics Analysis Pipeline

The two videos in this module will explain genetic data types, SMRT cells, DArT and ddRAD data and SNP arrays. We identify key-steps to create genomic data for conservation and provide an overview over the biggest sequence providers in Australia as of 2023 (AGRF, Ramaciotti, BRF, DArT etc).

5.1 Genetic data types and why are they useful?

5.2 Steps to creating genomic data

Module 6 Genome Assembly and Annotation

This module provides an overview of genome assembly and annotation, including available tools and methods.

6.1 Genome and organelle assembly

6.2 Genome annotation

Module 7 Population Genetic Analysis and Outputs

This is the most technical of our modules. We look at aligning genomes and the impact of filtering on datasets. We then discuss metadata requirements and documenting analysis decisions. We also introduce the TSI biodiversity portal, an online tool to generate standard conservation genetics reports aligned to the genetic reporting requirements under the Convention for Biological Diversity (CBD).

7.1 Calling genetic variants

7.2 Impact of filtering on datasets

7.3 Metadata and documenting analysis decisions

7.4 TSI Biodiversity Portal

Module 8 Conservation Report and TSI Portal Outputs explained

After assembling and aligning the genomes in the previous modules, we now look at important population genetics metrics and the key aspects to look for in reports and outputs

8.1 Conservation genetics report explained

8.2 Key outputs to look out for in the report

Module 9 End-to-end case studies – genetics into conservation management

In this module we will introduce a range of Australian conservation projects that have used genetic data during their decision making processes.

9.1 Tasmanian Devil

9.2 Christmas Island lizards

9.3 Myrtle rust in scrub stringybark and broad-leaved paperbarks

9.4 Helmeted honeyeater

9.5 Macquarie Perch

9.6 Corals

9.7 SNP array case study

9.8 eDNA

9.9 Button wrinkelwort

Module 10 End-to-end case studies – Genetic into ecology research

This module introduces ecological research projects that have used genetic data to inform their ecological datasets.

10.1 Superb Parrots

10.2 Southern hairy-nosed wombat

10.3 Ghost Bat