The Genetic Rescue Foundation Blog

Science Exchange enables completion of the Kakapo 125 Project

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To date, The Genetic Rescue Foundation’s Kakapo 125 Project has successfully sequenced 80 kākāpō. This work was made possible by collaborating with DNA sequencing service providers on the Science Exchange network. In addition to enabling The Genetic Rescue Foundation to easily access the world’s best service providers we’re thrilled to announce that Science Exchange will be funding the remainder of the project in order to bring it to completion!

Detailed genetic data for every individual in an entire species is a world first and represents a genomics-focused paradigm shift in modern conservation efforts. The possible discoveries that will come from this rich dataset are limitless. Scientists’ immediate efforts will be focused on finding genetic links to dwarfism, infertility and other diseases and conditions hampering kākāpō population recovery.

Read the full article

Predator-free target our last chance to save the kiwi

New Zealand will succeed in its ambition to be predator free by 2050 because the alternative is unthinkable to New Zealanders.

Unless we grasp the opportunity to fight back against these insidious invaders there will be no kiwi left by 2050. No kea, no kaka or kokako. We’ll be lucky to have a few fantails in the garden.

The decline of our native birds, insects and reptiles has been so steep, and the increase in predator populations so marked, that this campaign really is our last chance to save from extinction the things we treasure, and which make New Zealand special and different.

Read the full article

“Unexpected mutations after CRISPR-Cas9 editing in vivo” are most likely pre-existing sequence variants and not nuclease-induced mutations

Here we demonstrate that the simplest interpretation of Schaefer et al.’s data is that the two CRISPR-Cas9-treated mice are actually more closely related genetically to each other than to the control mouse. This strongly suggests that the so-called “unexpected mutations” simply represent SNPs and indels shared in common by these mice prior to nuclease treatment. In addition, given the genomic and sequence distribution profiles of these variants, we show that it is challenging to explain how CRISPR-Cas9 might be expected to induce such changes. Finally, we argue that the lack of appropriate controls in Schaefer et al.’s experimental design precludes assignment of causality to CRISPR-Cas9. Given these substantial issues, we urge Schaefer et al. to revise or re-state the original conclusions of their published work so as to avoid leaving misleading and unsupported statements to persist in the literature.

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GRF Partner Science Exchange Raises $28M USD

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The Genetic Rescue Foundation heavily makes use of the Science Exchange platform to locate the best service providers to complete its research. We’re thrilled to announce that Science Exchange has successfully raised $28M USD to continue its expansion in the outsourced R & D sector.

Read the full article on Forbes.com

Four in five of NZ’s native birds ‘in trouble’

  • 32 per cent of NZ’s 168 native bird species “in serious trouble”
  • Another 48 per cent of native birds “in some trouble”
  • Environment watchdog recommends big funding boost, possibly through a levy on tourists
  • Also recommends eradication of feral cats, genetic techniques, and ongoing 1080 use

Read the full article

Kakapo Genome Project – Second 40 kākāpō sequenced

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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.

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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.

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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.

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“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.

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NGOs enter the discussion

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

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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?

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David Iorns

Founder of Genetic Rescue

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