The Genetic Rescue Foundation Blog

Darwin: a genomics co-processor provides up to 15,000x acceleration on long read assembly

Genomics is transforming medicine and our understanding of life in fundamental ways. Genomics data, however, is far outpacing Moore’s Law. Third-generation sequencing technologies produce 100× longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. Over 1,300 CPU hours are required for reference-guided assembly of the human genome, and over 15,600 CPU hours are required for de novo assembly. This paper describes “Darwin” — a co-processor for genomic sequence alignment that, without sacrificing sensitivity, provides up to 15,000× speedup over the state-of-the-art software for reference-guided assembly of third-generation reads. Darwin achieves this speedup through hardware/algorithm co-design, trading more easily accelerated alignment for less memory-intensive filtering, and by optimizing the memory system for filtering. Darwin combines a hardware-accelerated version of D-SOFT, a novel filtering algorithm, with a hardware-accelerated version of GACT, a novel alignment algorithm. GACT generates near-optimal alignments of arbitrarily long genomic sequences using constant memory for the compute-intensive step. Darwin is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.

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Science is being surrendered to cultural sensitivity

In 2010 New Zealand’s venerable science body, the Royal Society of New Zealand, amalgamated with the Humanities Council. Science doesn’t have all life’s answers. Where would we be without literature, art, music, diverse cultures and the work of humanities scholars? But warm, fuzzy talk of inclusion and connection papered over a fundamental and long-standing philosophical clash.

Most scientists believe their scientific method is a superior way of building factual knowledge and, through technology, contributing to humankind’s material well-being.

What other human endeavours have delivered the internet, space exploration, organ-transplantation or knowledge of natural selection and continental drift?

This is self-evident to the public, but many in the humanities dismiss the scientific stance as “Western arrogance” and consider science is merely one of many world-views, all equally valid.

The “Western arrogance” idea, and a revisionist interpretation of the Treaty of Waitangi, are presumably behind the policy at the University of Otago that all research proposals by its scientists must be vetted by a Maori committee. In similar vein, the draft of the Royal Society’s new code of conduct now places the Treaty central to the society’s work.

There follows a proposal that New Zealand zoologists should “partner with Maori” whenever they study native animals. This goes too far.

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Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines

The population extinction pulse we describe here shows, from a quantitative viewpoint, that Earth’s sixth mass extinction is more severe than perceived when looking exclusively at species extinctions. Therefore, humanity needs to address anthropogenic population extirpation and decimation immediately. That conclusion is based on analyses of the numbers and degrees of range contraction (indicative of population shrinkage and/or population extinctions according to the International Union for Conservation of Nature) using a sample of 27,600 vertebrate species, and on a more detailed analysis documenting the population extinctions between 1900 and 2015 in 177 mammal species. We find that the rate of population loss in terrestrial vertebrates is extremely high—even in “species of low concern.”

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Can We Revive Extinct Species Like the Dodo?

Reviving extinct species is a trope of science fiction, but real-life scientists are working on every stage of the problem today. Meeting scientists focused on uncovering ancient animal genomes, or reviving individual cells to conserve species still around, Marnie Chesterton seeks out whether new technologies might, just possibly, bring back the iconic dodo.

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What a moa wants

As the dust has settled on another New Zealand election and policy promises turn into policy implementation, it seemed worthwhile to reflect on what a fully restored ecosystem would look like in 21st century Aotearoa/NZ and how this might happen.  What you might find surprising is how many of the proposals would actually have real merit if applied the right way.  Let’s start with the matter of what I mean by a “fully restored ecosystem”.  

By far the overwhelming consensus in the scientific community is that the New Zealand archipelago had a fully functioning and healthy ecosystem, until around 700 years ago when the first humans set up camp.  Almost all of the land was fully forested including the dry Eastern areas such as Hawke’s Bay, Marlborough and Canterbury.  Our Polynesian forebears did what humans do – they hunted and modified the landscape with fire. Much like our European ancestors later, these first settlers undoubtedly had no grasp on the magnitude of the change they were initiating.  Such was the scale of the fires that when historic records began in the early 19th century, many of the once forested areas were so distant from seed sources that they simply grew tussock grass and the forests never recovered.  So, what about the ecosystem in the wet areas?  Evidence suggests that many of these too were burned at various points but experienced far less devastating fires.  Nonetheless, the ecosystem was subjected to new predation by rats, dogs and humans.  

But here’s the rub.  A large proportion of the pre-European extinctions were from these Eastern areas where only tiny pockets of dryland forest still remain and many of the affected bird species were large and required large ranges.  

What is immediately obvious when you step into a remnant dryland forest is how dramatically different it is from the bush that most of us are familiar with.  There is a plethora of endangered plants, many twiggy and divaricating, that are absent elsewhere. Many of these plants have presented a challenge to restoration efforts, being slow to recolonise surrounding land.  Exactly what role moa and other extinct species played in this ecosystem is really anyone’s guess but undoubtedly it will have been profound.  


In pre-human times, Molesworth Station was forested and supported several species of moa.

To create a picture, imagine an expanse of land like inland Marlborough or Canterbury with relatively open, tall forest of totara, matai, kanuka and hoheria.  Without high rainfall, the understory would be made up of dense twiggy shrubs such as have been found in moa crop remains.  Growth rates would have been very slow so when a large tree died, the open area would have persisted for a relatively long time.  Large birds like moa could therefore move easily through forests like this and so too a predator like Haast’s eagle.  

Genetic Rescue Foundation has been a big proponent of restoring Aotearoa/NZ’s pre-human ecosystem with the best that science has to offer.  Along with many other dedicated conservation groups, we recognise that an ecosystem is just that and that the removal of any component part can have devastating effect long term on the entire system.  The challenge with a completely devastated ecosystem is – where do you start?  In my opinion we must start with an idea of where we want to end up.  That calls for something of a “master plan” and unity between the many conservation groups.  We also have to be pragmatic about where we fit into the picture allowing for economic activity, farming etc.  This election, all major parties have expressed a desire to invest in science, a goal of making NZ predator free, planting trees and improving the lot of our endemic species.  As it would happen, all of these points are critical to a long term vision that includes restoration of our extinct species.  

Assuming adequate investment in our research programmes, the international de-extinction community is likely to begin delivering the first revived species within a decade.  Of course, the more rigorous our efforts, the longer this will take.  If this is to ever move beyond small birds suitable for island refuges, this must involve predator eradication on mainland New Zealand as proposed by Predator Free NZ.   Furthermore, we must begin large scale restoration of our Eastern dryland forests.  Large expanses of degraded land such as Molesworth Station would seem natural targets for any such effort.  Yet, another non-profit, Tane’s Tree Trust, has developed significant resources to support indigenous plantation forestry.  Perhaps the billion tree target by the new government could be made up from 100% indigenous species.  Lastly, a restored ecosystem requires us to invest in science and conservation.  There is an opportunity for New Zealand to become the world leader in avian conservation biotechnology, working on contracts from across the world.  And, we can’t be reviving one species while we let another slip into extinction.  Restoration efforts such as the Kakapo and Kiwi Recovery Programmes need adequate resourcing.  We can’t have critical research to support these efforts determined by lottery from an undersized funding pool.

Ultimately, moa need to be part of a restored ecosystem which isn’t missing other species.  So, speaking on behalf of all moa past and future, it’s time to work together on a shared goal for a restored Aotearoa/NZ and the sooner we get to it the better.

Manipulating the avian egg: applications for embryo transfer, transgenics, and cloning

In vitro production of germline chimeras and avian cloning may utilise the transfer of avian embryos from their original eggshell to a surrogate eggshell for culture during incubation. Such embryo transfer is valuable for avian cloning as the only alternative would be to transfer the cloned avian embryos into the infundibulum of recipient birds. Given the advances in paleogenomics, synthetic biology, and gene editing, a similar approach might be used to generate extinct species, i.e. de-extinction. One objective of the present research was to examine if ratite eggs could be manipulated via windowing and sham injection, similar to that which could allow for avian genome manipulation and subsequent development. The efficiency of interspecific avian embryo transfer using Chicken (Gallus gallus domesticus) donor eggs and Turkey (Meleagris gallopavo) recipient eggshells was also investigated. Egg windowing and embryo transfer techniques utilised in the present research were adapted from those found in the scientific literature. Presumed fertile eggs from Rhode Island Red (n = 40), Silkie (n = 2), and White Leghorn Chickens (n = 18), Turkey (n = 48), Emu (Dromaius novaehollandiae) (n = 79), and Ostrich (Struthio camelus) (n = 89) were used in this research. Of the 41 Chicken eggs used for transfers into recipient Turkey eggshells, only one (2.4%) produced a chick. Of 31 windowed Emu eggs, one embryo survived for 25 d but no chicks were produced. Of 36 windowed Ostrich eggs, one embryo survived and hatched. The efficiency of the windowing and embryo transfers to produce chicks was low and further refinements are needed. Importantly, the results herein establish that manipulating ratite embryos is possible.

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Time to Spread Your Wings: A Review of the Avian Ancient DNA Field

Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions.

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