wild genomes

Ten awarded projects, summer 2020

We are pleased to announce the first awarded Wild Genomes projects. This was a competitive process and researchers were invited to address any conservation issue for any species as long as the resulting genomic data would be used for making applied conservation decisions. We received 58 applications from 19 countries and selected these 10 projects that will apply genomic technologies toward solving a wide variety of conservation problems. We’re excited to see genomic data used to improve outcomes for wildlife around the world.

JAGUAR

Principal Investigator: Paola Nogales Ascarrunz, Universidad Mayor de San Andrés Bolivia

The jaguar (Panthera onca) is a keystone species listed as Near Threatened by the International Union for Conservation of Nature (IUCN). The main threats for this species are habitat fragmentation, human-wildlife conflict, and illegal trafficking of its distinctive skins, as well as its claws and skull. Information on jaguar genetics is incomplete for Bolivia, and there is an urgent need to include genetic data in the species’ conservation action plan to be able to make evidence-based decisions.

This project aims to sequence 40 jaguar genomes to investigate genetic diversity, population structure, and gene flow. This will help identify areas in need of conservation actions (such as genetic rescue) and source populations for possible translocations. This is the first animal genomics project developed in Bolivia.

Joshua Tree

Principal Investigator: Jeremy Yoder, California State University Northridge

The Joshua tree (Yucca brevifolia) is an iconic keystone species of the Mojave Desert that is expected to experience dramatic reductions in suitable habitat under projected climate changes. However, the trees exist in a range of extreme climatic conditions, and populations may harbor genetic variation that could support adaptation to changing climate.

This project aims to produce whole-exome sequencing of 300 Joshua trees across species density, phenotypic and climatic diversity, and areas of special conservation concern. This will likely uncover genes related to the evolution of extremophile plants and thus allow mapping of genetic variants for climate adaptation and prediction of climate change susceptibility of existing Joshua tree populations.  The resulting genomic dataset will be the first of its kind for a keystone desert species and may serve as a model for genetically-informed desert conservation.

SUNFLOWER SEA STAR

Principal Investigators: Michael Dawson and Lauren Scheibelhut, University of California, Merced

In 2013, an outbreak of sea star wasting disease (SSWD) impacted over 20 species of sea stars. The sunflower sea star (Pycnopodia helianthoides), a keystone predator of urchins, was all but eradicated. The ecological loss—a 311% increase in urchin populations, a 30% decline in kelp forest density along the North American Pacific Coast—shows no sign of a rebound.

This project aims to discover genomic variation in the sunflower sea star that confers resilience to SSWD and other stressors. A fuller understanding will be gained of the genomic factors conferring high risk to SSWD, and the consequence of the 2013-2014 event on patterns of genomic diversity among remnant sea star populations. These insights will help shape a captive breeding program to advance genomic resilience in subsequent populations.

FIVE WHALES

Principal Investigator: Phil Morin, NOAA Fisheries, in collaboration with Vertebrate Genomes Project and San Diego Zoo Global Frozen Zoo

This project aims to ascertain biologically relevant information for these five whale species that represent evolutionary diversity across the cetacean phylogeny:

  • Gray whale (Eschrichtius robustus)—IUCN Endangered
  • False killer whale (Pseudorca crassidens)—IUCN Near Threatened
  • Amazon river dolphin (Inia geoffrensis)—IUCN Endangered
  • Blainville’s beaked whale (Mesoplodon densirostris)—IUCN data deficient
  • North Atlantic right whale (Eubalaena glacialis)—IUCN and ESA Endangered

The obtained reference genomes will help researchers determine taxonomy, demographic history, inbreeding, genome organization, and genes. This will also provide genomic resources for population-level studies and help to reveal breeding structure, epigenetic determination of age, stress and immune response,  local adaptation, and potential response to climate change.

TAKAHĒ

Principal Investigator: Lara Urban, University of Otago, in collaboration with the Vertebrate Genomes Project and the Takahē Recovery Programme, New Zealand

The takahē is the rarest and largest flightless rail in the world and is endemic to New Zealand. With the Murchison Mountains in Fiordland National Park as their only extant wild habitat, the species remains highly endangered. Once considered extinct, this species was rediscovered in 1948.

This project aims to first produce a platinum quality reference genome of the takahē in collaboration with the Vertebrate Genomes Project. Genomic sequencing data and pedigree analysis will reveal the genetic variation of the remaining population. These data will help to investigate and understand the genomic, phenotypic, microbial, and environmental factors that affect the fitness, persistence, and adaptive potential of the takahē. An extraordinarily detailed phenotypic and environmental dataset, cataloged by the Takahē Recovery Programme over decades, will empower a quantitative genomic approach rarely observed outside of humans, agricultural, or model species.

BINTURONG

Principal Investigator: Irhamna Putri Rahmawati, Yogyakarta Nature Conservation Foundation, Indonesia

Of the nine known subspecies of binturongs, four are endemic to Indonesia: Arctictis binturong pageli (Kalimantan), Arctictis binturong niasensis (Sumatra), Arctictis binturong kerkhoveni (Sumatra), and Arctictis binturong penicillatus (Java). Geographic isolation  caused binturongs to develop without genetic mixing. Maintaining these subspecies is important to the preservation of their genetic diversity.

Despite protected status, binturongs are routinely involved in the illegal wildlife trade. Yet returning rescued animals to their appropriate geographic origin proves difficult. This project aims to generate genetic markers that will be used to identify the island of origin. Later, these genetic markers will act as a tool to improve binturong conservation activities, such as reintroduction, rehabilitation, and captive breeding.

Eastern Quoll

Principal Investigator: Charles Feigin, University of Melbourne, Australia

The endangered Eastern quoll (Dasyurus viverrinus) is among the last extant mesopredators in Australia. With the extirpation of the last mainland populations of Eastern quolls in the 20th century, this marsupial species is now restricted to the island of Tasmania, at the far southern (coldest) end of its historical range. Efforts to translocate Eastern quolls from Tasmania to regions on the mainland are currently underway.

This project aims to generate a high-quality reference genome for the Eastern quoll and perform exome capture of individuals from several Tasmanian populations and captive-breeding sanctuaries, as well as from museum specimens of historical mainland populations. Initially, this information will help conservation managers maintain functional diversity in the populations and re-establish baseline mainland diversity as well. This may also help to guide the genetic management of the population for future climate warming.

CHINOOK SALMON

Principal Investigator: Mariah Meek, Michigan State University

The Chinook salmon (Oncorhynchus tshawytscha) is a keystone species of the Pacific Northwest. Human activity has caused dramatic declines in Chinook abundance and adaptive diversity. Efforts to conserve and restore wild populations are challenged by the extreme importance of local adaptation in the species.

This project aims to create a whole-genome, range-wide catalog of genomic diversity in Chinook salmon. This will facilitate the development of diagnostic assays for adaptive variation that can be applied to conservation issues such as restoring extirpated populations to historical habitats, informing conservation hatchery breeding programs, improving monitoring, and targeting conservation efforts that address species diversity.

SUN BEAR

Principal Investigator: Daniel W Förster, Leibniz Institute for Zoo and Wildlife Research, Germany

The sun bear (Helarctos malayanus) is a forest-dependent keystone species in its native Southeast Asian range. Despite its IUCN vulnerable status and serious conservation concerns, the sun bear is the least studied bear species. Its population genetic structure is unknown, and genetic monitoring is almost non-existent. Due to their rarity and elusiveness, it is difficult to obtain data on sun bear distribution, population size, and dynamics.

This project will generate a reference genome assembly to support research into the reproductive health of individuals used in ex-situ breeding-and-release programs, and the development of molecular tools to identify and genetically monitor at-risk populations.

Eastern long-toed salamander

Principal Investigator: Julie Lee-Yaw, University of Lethbridge, Canada

The eastern long-toed salamander (Ambystoma macrodactylum krausei) is extant at the edge of its range in Alberta, Canada. It is listed by the IUCN as a species of Special Concern.

In this project, population genomics data will be collected to inform source populations for reintroductions into sites where historical fish stocking programs had extirpated the species. Another opportunity is to study the effectiveness of under-road tunnels that have been installed to reduce salamander road mortality. Estimates of population connectivity may help inform the optimal placement of additional crossings.