Periodic Reporting for period 1 - ERODE (Evolutionary dynamics of genomic erosion and its application in biodiversity conservation)
Periodo di rendicontazione: 2023-06-01 al 2025-11-30
Biodiversity is declining at an alarming rate across the globe. As species face mounting pressures from habitat destruction, climate change, invasive species, and overexploitation, wildlife populations worldwide are undergoing dramatic declines. Amidst this crisis, conservation efforts have become increasingly urgent. Initial conservation strategies tend to focus on mitigating these threats and reversing population declines. Yet, there is another, less visible risk: the erosion of genetic diversity.
Genetic diversity underpins a species’ ability to adapt, survive disease, and respond to changing environments. When populations collapse, harmful mutations can accumulate, functional genetic variation is lost, and the substrate for future adaptation is compromised. These changes — known as genomic erosion — are difficult to detect without advanced tools, yet they can have lasting effects on a species’ long-term viability, even after population numbers have rebounded.
Our project, ERODE, aims to uncover how genomic erosion unfolds over time and to develop the tools needed to monitor and manage it. We focus on endangered species with well-documented conservation histories and use historical and modern genomes to reconstruct how their genetic health has changed. This allows us to assess not only how much genetic diversity has been lost, but also what that means for the future survival of these species.
ERODE combines evolutionary biology, genomics, and conservation science to address a key question: How can we better detect and manage the hidden genetic risks that threaten endangered species, even when their numbers appear to recover?
To do this, we are:
Reconstructing the evolutionary history of genetic diversity loss in multiple endangered bird species using museum specimens and modern samples;
Developing simulation tools and models to predict how genomic erosion evolves and affects species survival;
Designing practical genomic tools to guide conservation management, especially in captive breeding and reintroduction programs;
Exploring how genomic data can be integrated into international conservation assessments, such as the IUCN Red List and Green Status framework.
By linking the past to the present and building tools to guide future conservation efforts, ERODE contributes to a growing movement to make genomics a standard part of conservation planning. In the long term, our work supports more effective species recovery strategies and helps safeguard biodiversity in a rapidly changing world.
Genetic diversity underpins a species’ ability to adapt, survive disease, and respond to changing environments. When populations collapse, harmful mutations can accumulate, functional genetic variation is lost, and the substrate for future adaptation is compromised. These changes — known as genomic erosion — are difficult to detect without advanced tools, yet they can have lasting effects on a species’ long-term viability, even after population numbers have rebounded.
Our project, ERODE, aims to uncover how genomic erosion unfolds over time and to develop the tools needed to monitor and manage it. We focus on endangered species with well-documented conservation histories and use historical and modern genomes to reconstruct how their genetic health has changed. This allows us to assess not only how much genetic diversity has been lost, but also what that means for the future survival of these species.
ERODE combines evolutionary biology, genomics, and conservation science to address a key question: How can we better detect and manage the hidden genetic risks that threaten endangered species, even when their numbers appear to recover?
To do this, we are:
Reconstructing the evolutionary history of genetic diversity loss in multiple endangered bird species using museum specimens and modern samples;
Developing simulation tools and models to predict how genomic erosion evolves and affects species survival;
Designing practical genomic tools to guide conservation management, especially in captive breeding and reintroduction programs;
Exploring how genomic data can be integrated into international conservation assessments, such as the IUCN Red List and Green Status framework.
By linking the past to the present and building tools to guide future conservation efforts, ERODE contributes to a growing movement to make genomics a standard part of conservation planning. In the long term, our work supports more effective species recovery strategies and helps safeguard biodiversity in a rapidly changing world.
Since the start of the ERODE project, we have made substantial progress in understanding how genomic erosion unfolds and how it can be monitored and managed in conservation practice.
A major achievement has been the generation of high-quality reference genomes and time-series genomic datasets for multiple iconic endangered bird species, including the Mauritius kestrel, pink pigeon, echo parakeet, whooping crane, orange bellied parrot, swift parrot, little owl, seychelles paradise flycatcher and regent honeyeater. These datasets are built from a unique combination of historical specimens (some over 150 years old) and modern samples. They allow us to directly compare past and present genomes, providing unprecedented insights into how genetic diversity changes over time in response to population decline and recovery.
We have also developed novel simulation models that recreate how genomic erosion unfolds in shrinking and fragmented populations. These include spatially explicit models that account for habitat loss and movement of individuals, and predictive tools to explore the long-term consequences of reduced genetic diversity. Our work shows that genomic erosion often continues long after populations start to recover.
In addition, we created tools to estimate the burden of harmful mutations in endangered species, even when they lack well-annotated genomes. One of our methods, called LiftLoad, allows researchers to transfer mutation impact scores from domestic species (like chickens) to their wild relatives. These tools make it possible to design genomics-informed breeding strategies, helping conservation managers retain healthy genetic variation while reducing genetic load.
Another important contribution has been the creation of an open-access comparative genomics framework for assessing genetic erosion across species. This framework is available to the research community and supports reproducibility and collaboration across projects.
We are also working to bring genomics into formal conservation assessment tools, such as the IUCN Green Status framework. Our proof-of-concept models illustrate how genetic data can be integrated into global conservation evaluations, helping assess not only extinction risk but also the genetic resilience of populations.
These achievements position ERODE at the forefront of a new wave in conservation science — one that moves beyond numbers alone and incorporates evolutionary and genetic processes into how we protect biodiversity.
A major achievement has been the generation of high-quality reference genomes and time-series genomic datasets for multiple iconic endangered bird species, including the Mauritius kestrel, pink pigeon, echo parakeet, whooping crane, orange bellied parrot, swift parrot, little owl, seychelles paradise flycatcher and regent honeyeater. These datasets are built from a unique combination of historical specimens (some over 150 years old) and modern samples. They allow us to directly compare past and present genomes, providing unprecedented insights into how genetic diversity changes over time in response to population decline and recovery.
We have also developed novel simulation models that recreate how genomic erosion unfolds in shrinking and fragmented populations. These include spatially explicit models that account for habitat loss and movement of individuals, and predictive tools to explore the long-term consequences of reduced genetic diversity. Our work shows that genomic erosion often continues long after populations start to recover.
In addition, we created tools to estimate the burden of harmful mutations in endangered species, even when they lack well-annotated genomes. One of our methods, called LiftLoad, allows researchers to transfer mutation impact scores from domestic species (like chickens) to their wild relatives. These tools make it possible to design genomics-informed breeding strategies, helping conservation managers retain healthy genetic variation while reducing genetic load.
Another important contribution has been the creation of an open-access comparative genomics framework for assessing genetic erosion across species. This framework is available to the research community and supports reproducibility and collaboration across projects.
We are also working to bring genomics into formal conservation assessment tools, such as the IUCN Green Status framework. Our proof-of-concept models illustrate how genetic data can be integrated into global conservation evaluations, helping assess not only extinction risk but also the genetic resilience of populations.
These achievements position ERODE at the forefront of a new wave in conservation science — one that moves beyond numbers alone and incorporates evolutionary and genetic processes into how we protect biodiversity.
The ERODE project is delivering tools and insights that have the potential to reshape how conservation decisions are made. By making it possible to track and predict genetic risks over time, our results directly support better-informed species recovery and reintroduction strategies.
Potential impacts include:
Improving conservation outcomes by identifying populations at risk not only from demographic threats but from invisible genetic decline;
Enhancing the design of captive breeding programs to maintain genetic health and reduce harmful mutations;
Informing international conservation policy by integrating genetic data into global tools like the IUCN Red List and Green Status assessments;
Establishing practical, open-access pipelines for applying comparative genomics and predictive simulations across species.
Our work supports the growing recognition that genetic diversity is a critical component of biodiversity — one that must be protected to ensure long-term species survival. The tools and data produced through ERODE can help conservation managers anticipate genomic risks and act before they become irreversible.
To ensure further uptake and long-term success, several key needs have been identified:
Continued investment in genomic monitoring and long-term sampling programs, especially in data-poor regions;
Training and capacity-building for conservation practitioners, to ensure that genomic tools can be implemented in real-world settings;
Stronger integration between science and policy, particularly in updating conservation standards to include genomic data;
International collaboration to harmonize data sharing, ethical standards, and sample access across borders and institutions.
While ERODE is focused on endangered birds, the approaches we are developing are transferable to a wide range of species and ecosystems. They can also support the conservation of commercially, culturally, or ecologically important species that are not yet threatened but may be at risk in the future.
Potential impacts include:
Improving conservation outcomes by identifying populations at risk not only from demographic threats but from invisible genetic decline;
Enhancing the design of captive breeding programs to maintain genetic health and reduce harmful mutations;
Informing international conservation policy by integrating genetic data into global tools like the IUCN Red List and Green Status assessments;
Establishing practical, open-access pipelines for applying comparative genomics and predictive simulations across species.
Our work supports the growing recognition that genetic diversity is a critical component of biodiversity — one that must be protected to ensure long-term species survival. The tools and data produced through ERODE can help conservation managers anticipate genomic risks and act before they become irreversible.
To ensure further uptake and long-term success, several key needs have been identified:
Continued investment in genomic monitoring and long-term sampling programs, especially in data-poor regions;
Training and capacity-building for conservation practitioners, to ensure that genomic tools can be implemented in real-world settings;
Stronger integration between science and policy, particularly in updating conservation standards to include genomic data;
International collaboration to harmonize data sharing, ethical standards, and sample access across borders and institutions.
While ERODE is focused on endangered birds, the approaches we are developing are transferable to a wide range of species and ecosystems. They can also support the conservation of commercially, culturally, or ecologically important species that are not yet threatened but may be at risk in the future.