Little Less Conversation, a Little More Reading
This is not an exhaustive list of references, rather a bijou bibliography of websites, papers and articles that I have found helpful. If you want to find out more about de-extinction, the best place to start is the website of Revive and Restore: reviverestore.org. It’s a brilliant resource – up-to-date, reader friendly, packed with info about ongoing projects and technology. It even has an Extinct Species Colouring Sheet.
Introduction: Bringin’ It Back
The first de-extinction: Folch, J. et al. First birth of an animal from an extinct subspecies (Capra pyrenaica pyrenaica) by cloning. Theriogenology 71 (6): 1026-34 (2009).
It inspired Jurassic Park, the discovery of cellular nuclei inside an amber-entombed fly: Poinar G. O. & Hess, R. Ultrastructure of 40-Million-Year-Old Insect Tissue. Science 215 (4537): 1241-1242 (1982).
These two papers are depressing but well worth the read. They describe the alarming state and rate of present-day extinctions: (1) Dirzo, R. et al. Defaunation in the Anthropocene. Science 345 (6195): 401-406 (2014). (2) Urban, M. C. Accelerating extinction risk from climate change. Science 348 (6234): 571-573 (2015).
In 2013, there was a TEDx event all about de-extinction. Organised by Stewart Brand and Ryan Phelan from Revive and Restore – you can watch it here: www.longnow.org/revive/events/tedxdeextinction/the-program/
Chapter 1: King of the Dinosaurs
The paper that kicked it all off. Mary Schweitzer discovers structures that ‘look like’ red blood cells inside fossilised dinosaur bone, prompting speculation that organic matter can survive the fossilisation process: Schweitzer M. H. et al. Haem compounds in dinosaur trabecular bone. PNAS 94 (12): 6291-6296 (1997).
Critics attempt to pan Schweitzer’s work: Pevzner, P. A. et al. Comment on ‘Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry.’ Science 321 (3892): 1040 (2008).
But it seems that organic matter may survive the fossilisation process more often than we think: Bertazzo, S. et al. Fibres and cellular structures preserved in 75-million-year-old dinosaur specimens. Nature Communications 6: 7352 (2015).
The first ancient DNA to be recovered: Higuchi, R. et al. DNA sequences from the quagga, an extinct member of the horse family. Nature 312: 282-284 (1984).
And the prize for the oldest DNA discovered so far goes to … a horse: Orlando L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499: 74-78 (2013).
Has Schweitzer found evidence for DNA preservation in a T. rex fossil? The jury is out: Schweitzer, M. H. et al. Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules. Bone 52 (1): 414-423 (2013).
Jack Horner’s plans to build a dinosaur revealed in: Horner, J. & Gorman, J. 2010. How to Build a Dinosaur: The New Science of Reverse Evolution. Plume, New York City.
Not quite a dinosaur but a seriously ugly bird. Scientists create a chicken embryo with a snout: Bhullar, B-A. S. et al. A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history. Evolution 69 (7): 1665-1677 (2015).
Chapter 2: King of the Cavemen
Svante Pääbo is the first to retrieve DNA from a Neanderthal: Krings M. et al. Neanderthal DNA Sequences and the Origins of Modern Humans. Cell 90: 19-30 (1997).
Svante Pääbo is an ingenious, talented and inspirational scientist. No one tells his story better than the man himself: Pääbo, S. 2014. Neanderthal Man: In Search of Lost Genomes. Basic Books, New York.
Hendrik Poinar extracts nuclear DNA from fossil sloth poo: Poinar, H. Nuclear gene sequences from a late Pleistocene sloth coprolite. Current Biology 13 (13): 1150-1152 (2003).
It’s a draft but apparently that’s OK. Green, R. E. et al. A draft sequence of the Neanderthal genome. Science 328 (5979): 710-722 (2010).
The New York Times reports that a Neanderthal could be made for US$30million: Feb 12, 2009. www.nytimes.com/2009/02/13/science/13neanderthal.html
Hugely entertaining: Wynn, T. & Coolidge, Frederick L. 2012. How to Think Like a Neanderthal. Oxford University Press, Oxford.
Evidence that Neanderthals and modern humans interbred: Vernot, B. & Akey, J. M. Resurrecting Surviving Neanderthal Lineages from Modern Human Genomes. Science 343 (6174): 1017-1021 (2014).
Chapter 3: King of the Ice Age
An insight into the mind and works of one of the world’s most brilliant geneticists. George Church has speculated about de-extincting a Neanderthal and is busy making a cold-loving elephant: Church, G. & Regis, E. 2012. Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. Basic Books, New York.
The early days of mammoth de-extinction: Stone, R. 2003. Mammoth: The Resurrection of an Ice Age Giant. Fourth Estate, London.
That bloody mammoth: Grigoriev, S. et al. Discovery of a woolly mammoth (Mammuthus primigenius) carcass from Malyi Lyakhovski Island (New Siberian Islands). Scientific Annals of the School of Geology, Aristotle University of Thessaloniki 102: 64-76 (2014).
I’m always finding things that I’d forgotten about at the bottom of my deep freeze. Here’s what to do if you find a dead mouse in yours: Wakayama, S. et al. Production of healthy cloned mice from bodies frozen at -20°C for 16 years. PNAS 105 (45): 17318-17322 (2008).
A load of old bull. Japanese scientists clone livestock from frozen testicles: Hoshino, Y. et al. Resurrection of a Bull by Cloning from Organs Frozen without Cryoprotectant in a −80°C Freezer for a Decade. PLoS One 4 (1): e4142 (2009).
Researchers inject mammoth nuclei into mice eggs but not a squeak: Kato, H. et al. Recovery of cell nuclei from 15,000 years old mammoth tissues and its injection into mouse enucleated matured oocytes. Proceedings of the Japan Academy Series B Physical and Biological Sciences 85 (7): 240-247 (2009).
Scientists may not have de-extincted the woolly mammoth, but they have de-extincted one of its proteins: Campbell, K. L. et al. Substitutions in woolly mammoth haemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics 42: 536-540 (2010).
The woolly mammoth genome: Lynch, V. J., et al. Elephantid genomes reveal the molecular bases of Woolly Mammoth adaptations to the arctic. Cell Reports 12 (2): 217–218 (2015).
It’s the stuff that patent battles are made of – Jennifer Doudna and Emmanuelle Charpentier use CRISPR to cut the genome with extreme precision: Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337 (6096): 816-821 (2012).
No one asks the paleoecologists what they think about bringing Ice Age animals back, but they should. Jacquelyn Gill has some eloquent thoughts on de-extincting the woolly mammoth in her blog: https://jacquelyngill.wordpress.com/
Chapter 4: King of the Birds
Everything you ever need to know about dodo history: Fuller, E. 2002. Dodo: From Extinction to Icon. HarperCollins, London, New York.
From historical records, the date of the dodo’s demise can be calculated: Hume, J. P. et al. Palaeobiology: Dutch diaries and the demise of the dodo. Nature 429 (2004).
DNA analysis reveals that the dodo is officially a pigeon: Shapiro, B. et al. Flight of the Dodo. Science 295 (5560): 1683 (2002).
Recent excavations in Mauritius are revealing more about the dodo and its ecology: Hume, J. P. The Dodo: from extinction to the fossil record. Geology Today 28 (4): 147-151 (2012).
The Great Passenger Pigeon Comeback, everything you need to know: www.longnow.org/revive/projects/the-great-passenger-pigeon-comeback/
Everything you ever wanted to know about the passenger pigeon: Fuller, E. 2015. The Passenger Pigeon. Princeton University Press, New Jersey.
DNA tickled from passenger pigeon toe pads: Fulton, T. L. et al. Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon. Methods in Molecular Biology 840: 29-35 (2012).
Thinking about cloning a clucker? Then you need to know how to spot an egg’s DNA against its blobby, yellow background: Kjelland, M. E. et al. Avian cloning: Adaptation of a technique for enucleation of the avian ovum. Avian Biology Research 7 (3): 131-138 (2014).
A duck fathers a chicken … honestly, it really did: Liu, C. et al. Production of Chicken Progeny (Gallus gallus domesticus) from Interspecies Germline Chimeric Duck (Anas domesticus) by Primordial Germ Cell Transfer. Biology of Reproduction 86 (4): 101, 1–8 (2012).
Beautifully written, well worth a read: Avery, M. 2014. A Message From Martha: The Extinction of the Passenger Pigeon and Its Relevance Today. Bloomsbury, London, New York.
Chapter 5: King of Down Under
Paddle, R. 2000. The Last Tasmanian Tiger: The History and Extinction of the Thylacine. Cambridge Press, Cambridge.
Fuller, E. 2013. Lost Animals: Extinction and the Photographic Record. Bloomsbury, London, New York.
Schuster, S. C. et al. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research 19 (2): 213-220 (2009).
Thylacine DNA lives again: Pask, A. J. et al. Resurrection of DNA function in vivo from an extinct genome. PLoS One 32 3 (5): e2240 (2008).
On the global frogocalypse: Skerratt, L. F. et al. Spread of chytridiomycosis has caused the rapid global decline and extinction of frogs. EcoHealth 4: 125 (2007).
A frog cloning classic: Briggs, R. & King, T. J. Transplantation of living nuclei from blastula cells into enucleated frogs’ eggs. PNAS 38 (5): 455-463 (1952).
Chapter 6: King of Rock ’n’ Roll
If you want him, come sign here … the glorious, the one and only ‘Americans for Cloning Elvis’: americansforcloningelvis.bobmeyer99.com/
Find out more about Joni Mabe’s Panoramic Encyclopaedia of Everything Elvis at: www.roadsideamerica.com/story/16788
Hairy genomes … the first nuclear genome recovered from ancient hair: Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-762 (2010).
The 1000 Genomes Project: http://www.1000genomes.org/
A classic twins study: Bouchard, T. J. et al. Sources of Human Psychological Differences: The Minnesota Study of Twins Reared Apart. Science 250 (4978): 223-228 (1990).
Fifty years of nature versus nature: Polderman, T. J. C. et al. Meta-analysis of the heritability of human traits based on fifty years of twin studies. Nature Genetics 47: 702-709 (2015).
A genetic component to musical ability: Vinkhuyzen, A. A. et al. The Heritability of Aptitude and Exceptional Talent Across Different Domains in Adolescents and Young Adults. Behavior Genetics 39 (4): 380-392 (2009).
How is it that identical twins end up different? A piece that I wrote for New Scientist: Pilcher, H. The third factor: Beyond nature and nurture. New Scientist, 28 August (2013).
Poor parenting influences epigenetics influences how your pups turn out: Weaver, I. C. G. et al. Epigenetic reprogramming by maternal behaviour. Nature Neuroscience 7: 847-854 (2004).
This study shows how identical twins can sometimes become more different epigenetically with time: Talens, R. P. et al. Epigenetic variation during the adult lifespan: cross-sectional and longitudinal data on monozygotic twin pairs. Aging Cell 11 (4): 694-703 (2012).
The epigenomes of naturally and artificially conceived twins are different: Loke, Y. J. et al. Association of in vitro fertilisation with global and IGF2/H19 methylation variation in newborn twins. Journal of Developmental Origins of Health and Disease 6 (2): 115-124 (2015).
Why, if you made an infinite number of Elvis’s and raised them all in the same Tupelo shack, they’d still turn out different every time: Freund, J. et al. Emergence of Individuality in Genetically Identical Mice. Science 340 (6133): 756-759 (2013).
Scientists use CRISPR to edit the genomes of human embryos: Liang, P. et al. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein & Cell 6 (5): 363-372 (2015).
Chapter 7: Blue Christmas
Conservationist Phil Seddon and colleagues discuss how best to select candidates for de-extinction: Seddon, P. J. et al. Reintroducing resurrected species: selecting DeExtinction candidates. Trends in Ecology & Evolution 29 (3): 140-147 (2014).
Scientists revive a 30,000-year-old Siberian virus: Legendre, M. et al.Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. PNAS 111 (11): 4274-4279 (2014).
Does a woolly mammoth need a lawyer?: Carlin, N. et al. How to Permit Your Mammoth: Some Legal Implications of ‘De-Extinction’. Stanford Environmental Law Journal (2014). stanford.io/1SBEOKE
The sad, sad story of the Yangtze River Dolphin: Turvey, S. 2009. Witness to Extinction: How we Failed to Save the Yangtze River Dolphin. Oxford University Press, Oxford.
Christmas Island rats wiped out by infectious disease: Wyatt, K. B. et al.Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease. PLoS One 3 (11): e3602 (2008).
The United States National Park Service on Yellowstone’s gray wolf re-introduction: www.nps.gov/yell/learn/nature/wolf-restoration.htm
Chapter 8: I Just Can’t Help Believing
How to grow the sperm of an endangered bird inside a chicken: Wernery, U. et al. Primordial germ cell-mediated chimera technology produces viable pure-line Houbara bustard offspring: potential for repopulating an endangered species. PLoS One 29: 5 (12): e15824 (2010).
Scientists have successfully cloned the endangered Esfahan mouflon. This paper reports on some of their early work: Hajian, M. et al. ‘Conservation cloning’ of vulnerable Esfahan mouflon: in vitro and in vivo studies. European Journal of Wildlife Research 57 (4): 959-969 (2011).
How to save the black-footed ferret?: Wisely, S. M. et al. A Road Map for 21st Century Genetic Restoration: Gene Pool Enrichment of the Black-Footed Ferret. Journal of Heredity 106 (5): 581-92 (2015).
Cataloguing genetic variation in living tigers and museum specimens: Mondol, S. et al. Demographic loss, genetic structure and the conservation implications for Indian tigers. Proceedings of the Royal Society B 280: 20130496 (2013).
Genetic methods could help save endangered species: Thomas, M. A. et al. Ecology: Gene tweaking for conservation. Nature 501 (7468): 485-486 (2013).
Some like it hot; scientists reveal genes that may help trout survive in warmer waters: Rebl, A. et al. Transcriptome profiling of gill tissue in regionally bred and globally farmed rainbow trout strains reveals different strategies for coping with thermal stress. Marine Biotechnology (NY) 15 (4): 445-460 (2013).
In the interest of balance, here’s Ben Minteer on the ethics of de-extinction: Minteer, B. Is it right to reverse extinction? Nature 509 (7500): 261 (2014).
Chapter 9: Now You See It
For the latest on the northern white rhino, head to the Ol Pejeta Nature Conservancy’s website: http://www.olpejetaconservancy.org/
Rhinos are ecosystem engineers: Waldram, M. S. et al. Ecological Engineering by a Mega-Grazer: White Rhino Impacts on a South African Savannah. Ecosystems 11: 101-112 (2008).
It’s not looking good for the world’s megaherbivores: Ripple, W. J. et al. Collapse of the world’s largest herbivores. Science Advances 1 (4), e1400103 (2015).
First attempts at rhino IVF: Hermes, R. et al. Ovarian superstimulation, transrectal ultrasound-guided oocyte recovery, and IVF in rhinoceros. Theriogenology 72 (7): 959-968 (2009).
How to persuade a rhino to ovulate: Hermes, R. et al. Estrus induction in white rhinoceros. Theriogenology 78 (6): 1217-1223 (2012).
Artificial insemination in rhinos: Hermes, R. et al. First successful artificial insemination with frozen-thawed semen in rhinoceros. Theriogenology 71 (3): 393-399 (2009).
Cellular alchemy, Shinya Yamanaka makes stem cells from skin cells: Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126 (4): 663-676 (2006).
Stem cells make eggs make live mice: Hayashi, K. et al. Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice. Science 338 (6109): 971-975 (2012).
A crash of rhino iPS cells are made: Ben-Nun, I. F. et al. Induced pluripotent stem cells from highly endangered species. Nature Methods 8: 829-831 (2011).