The Genetic Rescue Foundation Blog

Kakapo Genome Project – Second 40 kākāpō sequenced

Shopify-Frontpage-Trevor

The Kakapo Genome Project an effort to sequence the genomes of all known living kākāpō has passed the halfway point with 80 individuals now sequenced!

The project has been receiving worldwide media coverage. Here’s a selection of articles published about this groundbreaking work.

With approximately 70 individuals remaining to be sequenced it’s not too late to sponsor a kākāpō genome and help this project through to completion. All sponsors receive a DNA portrait made from the genome of the kākāpō you’ve sponsored.

Portraits

De-extinction: more hype than hope – A rebuttal

Helen Taylor a genetics researcher at the University of Otago recently published this blog post that attempts to discredit The Genetic Rescue Foundation’s objectives.

http://sciblogs.co.nz/wild-science/2017/03/08/de-extinction-hype/

The following is The Genetic Rescue Foundation’s response to this piece.

1m3lh5

I believe in reasoned debate about ideas and concepts backed up using facts. To that end I have attempted to craft this response with the objective of correcting the incorrect information contained within that article and to providing a counter argument to that which has been supplied.

De-extinction could come at the cost of preserving native species

This is true. You can insert effectively anything in place of the word de-extinction and it is also true. For example funding for schools, healthcare and infrastructure. The Genetic Rescue Foundation is a non profit organisation that is 100% funded by donations. We receive no government funding and do not seek to divert any such funding away from existing conservation initiatives. We strongly agree that conservation is preferable to de-extinction which is why our flagship Kakapo Genome Project is conservation focused.

This project is more than 80% funded by overseas contributions. Therefore in the case of the Genetic Rescue Foundation I would argue the opposite is true. The Genetic Rescue Foundation is facilitating conservation efforts in New Zealand that previously were not possible due to lack of funding using money sourced primarily from overseas donors. This money allows New Zealand researchers including ironically researchers at The University of Otago to perform conservation focused research that would otherwise have not been funded.

youre-welcome

“De-extinction” is not actually a thing

Tell that to the Pyrenean ibex.

The Pyrenean ibex became the first taxon ever to become unextinct on July 30, 2003, when a cloned female ibex was born alive and survived for several minutes, before dying from lung defects.

http://www.theriojournal.com/article/S0093-691X(08)00778-4/abstract

While I agree that the woolly mammoth project and the majority of the other de-extinction projects including those of The Genetic Rescue Foundation are focused on the creation of so called proxies I disagree we will never reach a point that the genetic differences between proxy and extinct species are so indistinguishable as to be scientifically identical.

This proxy tangent used as a common argument against de-extinction has more to do with definitively identifying what constitutes a species at the genetic level then it does de-extinction.

Detractors also enjoy throwing epigenetics into the mix claiming that even if the proxy and extinct organisms genomes are identical you can never fully consider them identical due to epigenetic considerations. Well if that’s the case then that tiger born in a zoo isn’t a tiger it’s a proxy as the removal of the species from its habitat has epigenetic effects.

1m3vao

NGOs enter the discussion

The Genetic Rescue Foundation (GRF), (the organisation behind the kakapo genome sequencing crowd-funding effort)

kakapo

Let me dispel the persistent misinformation around the Kakapo Genome Project and The Genetic Rescue Foundation’s role in it.

1. The Kakapo Genome Project (sequencing the genomes of all known living kakapo) was the brainchild of DoC Scientist Dr. Andrew Digby not the University of Otago or New Zealand Genomics Ltd (NZGL) despite published articles that suggest otherwise.

Sequencing the genomes of all known living kakapo was one of several proposed projects Andrew put forward to The Genetic Rescue Foundation in late 2015. Of the projects put forward The Genetic Rescue Foundation selected “sequencing the genomes of all known living kakapo” as the one most inline with our core objectives.

2. The Kakapo Genome Project is not really a crowd-funded project. The project is currently only 36% crowd-funded i.e. 64% exclusively funded by The Genetic Rescue Foundation. At the time of project completion we anticipate that figure will be closer to 10% crowd-funded.

To-date we have funded the project to the tune of ~$56,000 USD. $20,000 of that came from a crowdfunding project that The Genetic Rescue Foundation organised and managed using the crowdfunding platform of our partner Experiment.com. $29,000 came from private donations to The Genetic Rescue Foundation and $7,000 has come from the sale of kakapo genome sponsorships. 80%+ of those funds have come from outside of New Zealand.

The Genetic Rescue Foundation’s projects for de-extinction of New Zealand species are far more developed. GRF has already raised partial funds for moa genome sequencing. However, Craig Millar’s lab in Auckland has possibly beaten them to the punch on sequencing a moa genome.

What about our work to-date would suggest we are in any kind of race? We’re extremely excited about the prospect of any moa genome becoming available as my tweet which I wrote in 2015 (and Helen Taylor oddly referenced) suggests. Having a comprehensive annotated genome of the target species is the first step in most de-extinction efforts. Our moa de-extinction efforts are no different.

We are working on a moa genome because one is not yet available of sufficient quality for us to use. If someone else achieves that reference genome before The Genetic Rescue Foundation does and makes it publicly available no one will be happier than me. It will allow us to move on to the next research phase.

Ironically we’re primarily working on this moa genome with UCSC Paleogenomics i.e. Beth Shapiro’s lab. Given Helen Taylor correctly praises Beth’s industry leading expertise in the field of ancient DNA it’s unusual she’s so quick to heap derision on one of her collaborators namely The Genetic Rescue Foundation.

There is no mention that birds represent one of the most challenging groups for “de-extinction” because they lay eggs.

The fact that Helen Taylor would write that is tangible evidence that she did little more than skim our website before posting her article. We discuss in some detail the challenges involved with avian de-extinction on our site. Here’s an excerpt from our description of primordial germ cell introgression.

This is the most difficult and under developed part of the project. Assuming we have a complete sequence of the moa and the tinamou, we would need to know which moa sequences to insert and which to leave as tinamou. At this point, the essential differences between species are unknown. This is an exaggerated version of the quest to understand the differences between breeds within a species (e.g. a Pekinese and a Great Dane) at the sequence level. Currently we can target individual genes in the avian genome but targeting hundreds or thousands of genes would be beyond the capabilities of current technology. However it’s likely that de-extinction experiments will eventually overcome this problem.

https://www.geneticrescue.science/projects/de-extinction/moa

GRF’s intentions may be good, but their efforts seem somewhat misdirected.

So permit me to summarise our intentions.

The purpose of the Genetic Rescue Foundation is to advance the scientific techniques required to prevent species extinction through genetic intervention. We help talented scientists working on relevant projects to obtain funding and to connect with collaborators and institutions that will expedite their research.

In other words we exist to help conserve native species by funding scientists actively working on advancing genomic technologies.

Since late 2015 we’ve funded New Zealand based research institutions most of whom have been directly affiliated with the University of Otago to the tune of ~$70,000 NZD.

We have generated worldwide media attention by undertaking ambitious New Zealand focused and run research projects such as the Kakapo Genome Project a world first.

Yes we believe in advancing the science of de-extinction but only as part of a wider genomic toolkit for the preservation of biodiversity. We certainly do not advocate de-extinction as a replacement for conservation but in the case of many of our former native species that ship has sailed.

We feel our results speak for themselves and our efforts have plenty of direction.

What’s the danger in failing to back your own horse?

In summary the saddest aspect of Helen Taylor’s criticism of The Genetic Rescue Foundation is that it’s indicative of the desperate lows that scientific research in New Zealand has reached.

We’re a non profit organisation bringing non trivial sums of money in from overseas and commissioning exciting research in New Zealand involving New Zealand scientists and institutions.

Those efforts have been met with almost universally positive responses from all different types of people throughout New Zealand and the world.

Who have been the most active detractors of our efforts? New Zealand based scientists like Helen Taylor who’s own institution is actively benefiting from our achievements. Et tu, Brute?

david-iorns-compressor

David Iorns

Founder of Genetic Rescue

Welcome to Pleistocene Park

In Arctic Siberia, Russian scientists are trying to stave off catastrophic climate change—by resurrecting an Ice Age biome complete with lab-grown woolly mammoths.

Read the full article

Google makes significant donation to kākāpō conservation

New Zealand’s kākāpō recovery program has been given a major shot in the arm thanks to a significant donation from The Genetic Rescue Foundation supporter Stafford Marquardt and Google.

Read the full article

Half of the world’s species could become extinct, biologists say

Here’s the sobering truth: Around half the species on Earth today could disappear by middle of the century, unless we humans can tackle climate change and slow our population growth.

That’s a view shared by leading biologists and ecologists, many of whom are gathering in the Vatican this week for a wonky but optimistic-sounding conference: “How To Save the Natural World on Which We Depend.”

Read the full article

Woolly mammoth on verge of resurrection, scientists reveal

The woolly mammoth vanished from the Earth 4,000 years ago, but now scientists say they are on the brink of resurrecting the ancient beast in a revised form, through an ambitious feat of genetic engineering.

Speaking ahead of the American Association for the Advancement of Science (AAAS) annual meeting in Boston this week, the scientist leading the “de-extinction” effort said the Harvard team is just two years away from creating a hybrid embryo, in which mammoth traits would be programmed into an Asian elephant.

“Our aim is to produce a hybrid elephant-mammoth embryo,” said Prof George Church. “Actually, it would be more like an elephant with a number of mammoth traits. We’re not there yet, but it could happen in a couple of years.”

Read the full article

First Gene Drive in Mammals Could Aid Vast New Zealand Eradication Plan

Scientists working in coördination with a U.S. conservation group say they’ve established an evolution-warping technology called a “gene drive” in mammals for the first time and could use it to stamp out invasive rodents ravaging seabirds on islands.

Gene-drive technology, so far demonstrated only in insects and yeast, is a powerful way of biasing the inheritance of DNA such that wild animals can be genetically altered as they reproduce, including to cause a population crash.

Now two scientific teams—one in Australia and one in Texas—say they’ve genetically engineered the house mouse, Mus musculus, so that its genome also harbors genetic surprises that could be unleashed on wild populations. The modified rodents were born in the last two months and the results are still preliminary.

The effort to establish gene drives in mammals is being coördinated by Island Conservation, a hard-charging conservation group based in Santa Cruz, California, whose specialty is bombing small islands with rat poison in order to save endangered seabirds. Its motto is “preventing extinctions.”

Read the full article

%d bloggers like this: