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RADCamp Brisbane 2025

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Hands-on training in genomic analyses for biodiversity conservation (ID: 16)

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Laura Bertola - National Centre for Biological Sciences

Ilha Byrne - University of Queensland

Anubhab Khan - Indian Institute of Science

Matheus Mello Athayde - University of Queensland

Katharine Prata - Australian Institute of Marine Science

Isaac Overcast - Columbia University

Laura Tensen - University of Copenhagen

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ACKNOWLEDGEMENT OF COUNTRY

I acknowledge the Traditional Owners (Turrbal/Jagera) and their custodianship of the lands on which we meet.

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We pay our respects to their Ancestors and their descendants, who continue cultural and spiritual connections to Country.

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We recognise their valuable contributions to Australian and global society.

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Ice breaker: Join us!

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Tippler’s Tap��

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Intro to Conservation Genetics

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Led by Laura Bertola (National Centre for Biological Sciences)

Molecular Ecology Resources: Volume 25, Issue 5

Special Issue: Advancing species conservation and management through omics tools

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Loss of Biodiversity

Rogan et al., 2023

  • Primarily through loss of populations: mammals: loss of min. 30% (1900-2015) almost half: loss of >80%

(Ceballos et al., 2017)

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  • Not all range loss is equal (Rogan et al., 2023)

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Hoban, et al., Biological Reviews, 2022

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Genetic data

  • Diversity and connectivity
  • Identify individuals (population estimates, home ranges, connectivity)
  • Pedigrees, parentage
  • Hybridization
  • Population history and future trajectory
  • Prioritization, e.g. based on uniqueness or adaptive traits

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Bertola et al., Proc Roy Soc B, 2020

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Bertola et al., Proc Roy Soc B, 2020

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Intro to RADSeq Data

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Led by Isaac Overcast (Columbia University)

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Conservation Genetics Case Studies

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Led by Katharine Prata and Ilha Byrne

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Application of Conservation Genomics

Cryptic species = genetically distinct groups that are not easily recognisable by morphology

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Coral reef ecosystems are under severe threat from marine heat waves driven by climate change

March 2024, GeoNadir, Macquarie University

James Cook University

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Coral reef ecosystems are under severe threat from marine heat waves driven by climate change

Up to 97% mortality on some northern GBR reefs

Great need to understand thermal adaptation and demographic processes in corals for restoration and assisted evolution

Reef Restoration and Adaptation Program

June 2024, GeoNadir, Macquarie University

James Cook University

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Cryptic coral species & hybridisation: long recognised

But, genomic studies are revealing even more cryptic species, as more taxa get sequenced and where previous markers were unable to detect!

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Why should we care about cryptic species?

Assuming this is one species…

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Conclusion: This species can survive a wide range of temperatures

Temperature

Fitness

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Why should we care about cryptic species?

Temperature

Genomics reveals two species…

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Conclusion: Each species can survive a narrower range of temperatures

Assuming this is one species…

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Conclusion: This species can survive a wide range of temperatures

Can be any aspect of niche or species range

Fitness

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Possible issues for restoration arising from cryptic species

Taxon-environment mismatch

Competitive dominance

Reproductive failure

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Detecting closely-related cryptic species using repeatable genomic criteria*

Site 1

Site 2

Reproductive isolation (different species)

OR

differentiation by distance

No way to tell without experiments

*Differentiation detectable by PCA or Structure/Admixture

Riginos, … Byrne,… Prata (2024) Peer Community Journal

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Detecting closely-related cryptic species using repeatable genomic criteria*

Site 1

Site 2

Reproductive isolation (different species)

OR

differentiation by distance

Sympatry implies reproductive isolation

Riginos, … Byrne,… Prata (2024) Peer Community Journal

*Differentiation detectable by PCA or Structure/Admixture

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Detecting closely-related cryptic species using repeatable genomic criteria*

*Differentiation detectable by PCA or Structure/Admixture

Site 1

Site 2

Reproductive isolation (different species)

OR

differentiation by distance

Replication of sympatry

Sympatry implies reproductive isolation

Divergence amongst sympatric taxa greater than differentiation by dispersal

Riginos, … Byrne,… Prata (2024) Peer Community Journal

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How many studies have cryptic species?

Riginos, … Byrne… Prata (2024) Peer Community Journal

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Resolving cryptic species in corals on the GBR

Meziere, Popovic, Prata et al (2024) Evolutionary Applications

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Resolving cryptic species in corals on the GBR

Meziere, Popovic, Prata et al (2024) Evolutionary Applications

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Meziere, Popovic, Prata et al (2024) Evolutionary Applications

Resolving cryptic species in corals on the GBR

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Sympatric occurrence of genetically divergent taxa

Some evidence of association with different environments

Cryptic taxa exhibit different thermal tolerances (Meziere et al. unpublished)

Meziere, Popovic, Prata et al (2024) Evolutionary Applications

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Summary

  • Cryptic species are ubiquitous in corals
  • Cryptic species are likely differentially adapted
  • For restoration or assisted gene flow make sure to consider the implication of cryptic species on your strategy
  • If doing any coral study and unsure whether there are cryptic species make to preserve tissue for later genomic analysis

Riginos, … Byrne,… Prata (2024) Peer Community Journal

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Reef Restoration and Adaptation Program

But genomics tools, like RADseq and WGS can help us unravel the complexity of coral species

According to GoogleScholar there are 1.6 million coral studies and we still don’t have a firm grasp on who mates with whom!

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Assessing inbreeding in Australian fairy wrens

Anne Peters and her team at Monash have been running a long-term study on a population at Mornington Wildlife Sanctuary (AWC) since 2004.

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Assessing inbreeding in Australian fairy wrens

Purple-crowned fairy-wren western subspecies is listed as Endangered

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DArTseq has recently been used to both validate the population pedigree (parentage reconstruction) and estimate genomic inbreeding

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Assessing inbreeding in Australian fairy wrens

Lifetime fitness consequences of genomic inbreeding

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Assessing inbreeding in Australian fairy wrens

Jennifer Evans (soon to be Dr. Evans!)

Jennifer.Evans@anu.edu.au

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Intro to Seadragons

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Led by Laura Tensen (University of Copenhagen)

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Seadragons: a case study

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https://radcamp.github.io/Brisbane2025/