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Wild Genomes: How Genomic Insights Are Helping To Protect Endangered Species

Wild Genomes: How Genomic Insights Are Helping To Protect Endangered Species  content piece image
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Extinction rates today are much higher than would be expected due to natural background rates, a situation thought to be a result of increasing human driven environmental pressures such as deforestation and climate change. Currently, more than 38,500 species are threatened with extinction, representing 28% of all assessed species. Conservationists are working tirelessly to protect endangered populations and prevent a further decline in biological diversity. The use of genomic tools, such as high-quality reference genomes, is starting to play a crucial role in this work.

Wildlife conservation organization
Revive & Restore is supporting scientists working to use genomics to protect biodiversity through its Wild Genomes program, part of which is backed by de novo genome assembly provider Dovetail Genomics. Their first collaborative project, "A Genome for Basuki,” will focus on conservation efforts for the Banggai cardinalfish of Indonesia, and plans for a second joint project, “A Genome for Laura,” were recently announced.

Technology Networks
had the pleasure of speaking with Revive & Restore’s program manager, Dr. Bridget Baumgartner, and Dovetail Genomics’ CEO, Todd Dickinson, to learn more about the program and its aims. Baumgartner and Dickinson also highlighted the value of genomic information in conservation efforts to manage endangered populations.

Anna MacDonald (AM): Can you tell us more about Revive & Restore’s Wild Genomes program and its aims?

Baumgartner (BB): Genomic technology is a potentially powerful tool for improving the information used by conservation professionals to make wildlife management decisions. Despite the low cost and commercial availability of genomic sequencing, we often hear from conservationists that they are not including genomic insight in their species management programs. When we ask why, they cite a lack of familiarity with the technology, the potential applications, or they incorrectly assume that genome sequencing is cost prohibitive. We started Wild Genomes in an effort to build a portfolio of projects that demonstrate clear applications and measurable benefits of using genomic insight for wildlife management. Each project starts with the development of the basic resources, including a high-quality reference genome (if one does not exist) and/or population whole genome sequencing at a scale appropriate to the project. The projects end with a demonstration of how those resources can be used to make conservation efforts more effective, lower cost or less uncertain. We plan to use the results of these projects to help conservationists better understand how to access these new tools and put them to use for their ongoing wildlife management projects.

Dickinson (TD): When it comes to species conservation, the best starting point to understand an organism’s biology is a high-quality genome assembly. With a reference genome in hand, conservation biologists can begin population studies to understand the genetics of at-risk species. Working with Revive & Restore and their Wild Genomes Program, we are sequencing a potentially at-risk wolverine (Gulo gulo), nicknamed Laura.

Once Laura’s genome is available, conservation biologists can use it as a foundation to investigate wolverine populations in Canada, the United States and other countries. These studies will help biologists understand population size and demographics, gene flow and genetic diversity, as well as providing new opportunities to monitor wolverine populations over time.

AM: What role is Dovetail Genomics playing in the project?

Dovetail has been an important partner for Wild Genomes for several reasons:

1.       They provide technical expertise and advice needed for creating the highest quality reference genomes available today, from a broad taxonomic range of species.

2.       They enable us to use bulk pricing, which reduces the costs associated with creating reference genomes.

3.       They’ve helped us promote this program to potential proposers and the interested public.

4.       They give our projects early access to new sequence assembly products they are developing, often before they are commercially available. This ensures that the genomes we are producing are always cutting edge in terms of accuracy and completeness.

The Basuki and Laura reference genome efforts are being supported by Dovetail Genomics on behalf of our service project customers. Dovetail is donating $500 for every service project we sell until we sequence and assemble the wolverine genome. 

AM: How are species chosen for the program?

Wild Genomes is a competitive grant program. It is also currently topic-based, meaning we call for proposals that fit a specific description (for example, the last call was for marine species). Project ideas that fit the topic are reviewed for the following criteria:

        conservation need of the target species

        potential impact of the genomic resources

        technical feasibility

        ability to transition the results immediately for use in the field

AM: What issues does a lack of genomic information present for protecting endangered species?

There are many difficult questions that could potentially be more easily answered about endangered species with the addition of genomic insight. Here are a few examples:

        Taxonomic identity: Are the individuals of two adjacent populations the same species, or do they represent different subspecies?

        Genetic diversity: What is the effective population size for my species of interest? What are the current demographics?

        Genetic load: Are deleterious genes being fixed in the population?

        Gene flow: Are there sufficient sources of new genetic diversity or has the population become too isolated?

        Forensics and protection: What size is the habitat range of an individual of this species, or, from where are the poachers/pet-smugglers most active?

We are currently witnessing the planet’s sixth mass extinction event, making preserving biological diversity one of mankind’s most important responsibilities. As human-based pressures continue to threaten ecosystems, there has never been a greater need for tools to monitor, preserve and enhance biodiversity. High-quality, contiguous genome assemblies are crucial for conservationists to preserve threatened and at-risk species.

Accurate genome assemblies help us study inbreeding depression, admixture and introgression, population diversity maintenance, hybrid speciation, disease susceptibility, behavioral ecology, adaptive allele identification and genetic rescue.

Proximity ligation is key to creating chromosome length assemblies. While long-read sequencing platforms are improving assembly contiguity over short-reads, they have only reached chromosome scale for the smallest genomes.

Using Hi-C technology to apply proximity ligation to non-model organism de novo genome assembly, we have already delivered more than 1,600 high-quality genomes for many unique species, advancing research for hundreds of scientists. These assemblies support conservation efforts around the globe.

AM: In what ways can genomic insights help conservation scientists to manage endangered populations?

Genomic technology can provide information that cannot be ascertained by visual inspection to allow conservation professionals to make more informed and more confident decisions. For example, it can be hard to know whether or not a particular genetic intervention is warranted or likely to be successful based on the outward appearance or behavior of individual animals under management. Being able to accurately assess the gene pool, the degree of relatedness between individuals in a captive breeding program, or the amount of gene flow between adjacent populations in the wild could enable decisions that lead to the desired outcome for a conservation project. It is analogous to the use of genetic information for personalized medicine (is this individual pre-disposed to a particular disease, or are two individuals close relatives?), forensic investigations (how many people passed through this area, what are their gender and age distributions?), or ancestry analysis (is this individual a descendent of a people from a specific country?).

AM: Are there any plans to sequence already extinct species for de-extinction projects?

We are currently focused on acquiring genome sequences of endangered species. There are two ongoing de-extinction efforts at Revive & Restore (heath hen, and passenger pigeon). Draft genomes are available for both species, though we may upgrade them to higher quality with Dovetail in the future.

AM: How does the program fit into the Genetic Rescue Toolkit? Aside from sequencing, what other biotechnologies are needed for conservation efforts?

Genomics and biobanking are the two technologies that form the foundation of the genetic rescue toolkit. No other tools would be particularly useful without these resources. Genomics generally can be used to describe the specific genetic context for a given species under management. From there, the other tools in the kit can be employed as part of the solutions or interventions that are predicted to benefit the threatened species and improve its chance of survival.

Todd Dickinson and Dr. Bridget Baumgartner were speaking to Anna MacDonald, Science Writer for Technology Networks.