WILD GENOMES

AWARDED PROJECTS

We are pleased to announce the second round of Wild Genomes awards. Each awarded project receives funding for the development of genomic resources that are used to make applied conservation decisions. Through Wild Genomes, Revive & Restore is working to put the tools of genomics and biobanking into the hands of conservationists and wildlife managers around the world.

Awardees From The Wild Genomes–Marine Competition

 Gregory Piper, The Ocean Agency

SEA TURTLES OF THE WORLD

Principal Investigator: Camila Mazzoni, Leibniz Institute for Zoo and Wildlife Research; Co-PIs: Lisa Komoroske, University of Massachusetts Amherst; Oliver Berry, National Collections and Marine Infrastructure, Commonwealth Scientific and Industrial Research Organisation (CSIRO); Peter H. Dutton, National Oceanic and Atmospheric Administration (NOAA) Southwest Fisheries Science Center

The seven extant sea turtle species inhabit all oceans (except the polar regions) and face varying threats worldwide. Genetic tools provide a path for understanding key gaps in sea turtle conservation biology​—from identifying the origins of illegally traded sea turtle products to determining the turtles’ adaptive capacity under climate change. Yet reference genomes are available for just two sea turtle species: the Leatherback (Dermochelys coriacea) and Green (Chelonia mydas). This project will result in high quality, annotated reference genomes for the other five species:

  • Flatback (Natator depressus)—IUCN Insufficient Data
  • Hawksbill (Eretmochelys imbricata)—IUCN Critically Endangered
  • Kemp’s Ridley (Lepidochelys kempii)— IUCN Critically Endangered
  • Loggerhead (Caretta caretta)—IUCN Vulnerable
  • Olive Ridley (Lepidochelys olivacea)— IUCN Vulnerable

This collection will serve to unify conservation applications of genomic tools in the sea turtle community to attain top priority goals for population recovery and resilience. This project will serve as a model for similar projects that target larger groups of related species under management, particularly in the world’s developing regions.

BLACK-FOOTED ALBATROSS

Principle Investigator: Jessie Beck, Oikonos Ecosystem Knowledge; Co-PI: Diana Baetscher, NOAA Alaska Fisheries Science Center

This project will help address two major threats to the Black-footed albatross (Phoebastria nigripes): imminent loss of breeding habitat due to projected sea-level rise and incidental mortality in fisheries (“bycatch”).

Whole genome resequencing (WGS) of samples collected across six albatross breeding colonies in Hawaii and Japan will be used to characterize patterns of genetic differentiation. This is meant to help conserve the full diversity of the species while current translocation efforts are underway to establish colonies on islands protected from projected sea-level rise. WGS data will also inform genetic stock identification (GSI) of more than 700 albatross bycatch samples preserved over the past 10 years. Allele frequencies will help to assign the bycatch samples to natal breeding colonies. This project will be the first to empirically evaluate the impact of fisheries-caused mortality to individual Black-footed albatross colonies. It will also provide fisheries managers with previously unattainable information to help decrease the impacts of fisheries to the species.

 Oikonos Ecosystem Knowledge

 Taylor Frierson, Encyclopedia of Puget Sound

PINTO ABALONE

Principal Investigator: James Dimond, Western Washington University; Co-PI: Josh Bouma and Ryan Crim, Puget Sound Restoration Fund

After a 25-year fishery closure in Washington state, pinto abalone (Haliotis kamtschatkana) have failed to recover from overharvesting. However, 26,000 captive-bred, hatchery-produced abalone have been outplanted at several restoration sites and are showing promise. These hatcheries rely on abalone collected from Washington waters, but the local abalone is increasingly difficult to find. Broodstock from beyond Washington may be needed for continued restoration efforts.

This project will evaluate the population genetic structure of pinto abalone from Alaska to Mexico to inform the selection of new potential broodstock sources. Recently, the Puget Sound Restoration Fund (PSRF) has acquired pinto abalone samples from Alaska, British Columbia, Washington, and California. Additional samples from California and Oregon are being acquired. This award will support the sequencing and analysis of these samples using restriction site-associated DNA sequencing (RADseq).

JONAH CRABS

Principal Investigator: Andrea Bodnar, Gloucester Marine Genomics Institute

Historically considered a nuisance species, the Jonah crab is now gaining popularity as a seafood. Since the early 2000s, commercial landings of the species have grown tenfold.

This project will generate a Jonah crab reference genome to serve as a foundation for population genetic assessment throughout the species’ range (the Eastern seaboard from Canada to Florida). The population genetics combined with traditional tagging and landings data will be used to establish biologically relevant stock boundaries and serve as the foundation for a stock assessment. Ultimately, these data will be instrumental to ensure a sustainable, well-managed fishery. The reference genome will also serve as a valuable resource to expand understanding of Jonah crab biology and the capacity of these animals to respond and adapt to rapidly changing environmental conditions.

 Wanderingeden, iNaturalist (CC BY-NC)

 Paul Nicklen, Marinebio.org

NARWHALS

Principal Investigator: Marie Louis, GLOBE Institute, University of Copenhagen, Denmark

Although the global species abundance of the narwhal (Monodon monoceros) is over 100,000, several subpopulations are small and declining. The narwhal population in East Greenland suffers from unsustainable hunting: The proportion of females is decreasing, older males are overrepresented, and there is a lack of calves and juveniles. If this population disappears, it is unlikely others will recolonize the area. The loss of this top predator would affect the entire ecosystem and the Inuit communities who rely on them.

In this project, whole genomes from narwhals from different fjord systems in East Greenland will be re-sequenced to assess fine scale genetic structure, management units, local adaptation, and inbreeding. Such information is crucial for tailoring management plans and ensuring the persistence of subpopulations.

BROWN SEA CUCUMBER

Principal Investigator: Nina Overgaard Therkildsen, Cornell University

The brown sea cucumber (Isotichopus fuscus) was once the most conspicuous invertebrate in the shallow coastal waters of the Galápagos. However, intense overexploitation in the past three decades has decimated sea cucumber populations across the archipelago. The brown sea cucumber is now classified as endangered by the IUCN and listed under CITES.

This project will generate a chromosome-level genome assembly for the brown sea cucumber and use cost-effective, low-coverage whole genome re-sequencing to examine genome-wide patterns of variation among populations from all major bioregions in the Galápagos as well as three mainland reference populations. These resources will help prioritize local conservation efforts; guide re-introduction, supportive breeding, and genetic rescue programs; assess direct and indirect impacts of fishing and levels of local adaptation in the unique Galápagos marine ecosystem; and provide practical enforcement tools to combat poaching.

 Carmelo López Abad, iNaturalist (CC BY-NC)

 Charlie Veron, Corals of the World

MESOPHOTIC CORALS

Principal Investigator: Daniel Barshis, Old Dominion University; Co-PI: Veronica Radice, Old Dominion University

Given the various impacts affecting shallow coral populations, most notably climate change-induced coral bleaching, there is a potential role for mesophotic (‘middle light’) coral ecosystems in reef resilience. Located on deeper reefs, mesophotic coral species may avoid elevated seawater temperatures and/or contribute to coral resilience by maintaining local diversity and ecosystem function.

This project aims to produce reference genomes for two coral species Turbinaria peltata (pictured at left) and Montipora grisea, both mesophotic coral reef specialists of American Sāmoa. The reference genomes have direct application for a new conservation project with the National Park Service that is funded by the National Park Foundation and NOAA. The effort will test the thermal thresholds and investigate the climate change resilience of these two species.

Awardees From The First Wild Genomes Competition

A Xerces Blue specimen, dorsal and ventral orientations, collected from San Francisco’s Presidio on April 17, 1937 (Chris Grintner © California Academy of Sciences).

XERCES BLUE BUTTERFLY

Principal Investigators: Athena Lam, Chris Grinter, David J. Bettman, Matthew Van Dam, and Durrell D. Kapan, Center for Comparative Genomics and the Department of Entomology, California Academy of Sciences

The Xerces Blue (Glaucopsyche xerces), a small charismatic butterfly native to San Francisco’s dunes, was one of the first documented invertebrates to go extinct due to human-caused habitat destruction. This team seeks to identify a suitable ecological replacement for Xerces in San Francisco’s Presidio dunes, as part of a larger habitat restoration project led by the Presidio Trust.

To identify candidate replacements for Xerces, the team will extract DNA from and sequence the genomes of 80-to-100-year-old museum specimens of the extinct Xerces Blue* and its close relative, the Silvery Blue (Glaucopsyche lygdamus). The first Silvery Blue specimens to be sequenced will be from populations ecologically and geographically closest to Xerces: adapted to foggy coastal scrub and feeding on Xerces’ pea-plant host Deerweed (Acmispon glaber). Other Silvery Blues from populations more geographically and ecologically distant across a range of microclimates and host plants will also be sequenced. This will provide a genomic ‘measuring stick’ with which to localize Xerces amongst its closest living relatives and to identify one or more suitable candidate Silvery Blue populations for reintroduction.

Just as important as restoring food-web connections between native plants and butterflies, bringing back a ‘stand-in’ for the Xerces Blue is intended to spark our collective imagination, to generate a sense of hope, pride, and agency that humans can revive extinct ecosystem functions that are so critical to regenerating the planet.

*Xerces has been variously considered as a separate species (Glaucopsyche xerces) or as a subspecies of the Silvery Blue (Glaucopsyche lygdamus xerces), a question that this project will help resolve.

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. 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.

SIX WHALES

Principal Investigator: Phil Morin, NOAA Fisheries, in collaboration with Vertebrate Genomes Project and the Frozen Zoo at San Diego Zoo Wildlife Alliance

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
  • Pygmy sperm whale (Kogia breviceps)—IUCN Least Concern

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 (Porphyrio hochstetteri) 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.