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View Full Version : Dinosaur DNA reconstructed, but where is Jurassic Park?



Roger E. Moore
2018-Aug-27, 07:38 PM
https://www.nature.com/articles/s41467-018-04267-9

Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs

Rebecca E. O’Connor, Michael N. Romanov, Lucas G. Kiazim, Paul M. Barrett, Marta Farré, Joana Damas, Malcolm Ferguson-Smith, Nicole Valenzuela, Denis M. Larkin & Darren K. Griffin
Nature Communications (21 May 2018)

Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning.

Introduction: In the absence of cellular material and DNA from biological samples of long-extinct, early diverging lineages, data from genome sequence assemblies of extant species can nonetheless facilitate the reconstruction of gross genome structures (karyotypes). This can be achieved provided those assemblies are at, or close to, chromosome level, i.e. one scaffold per chromosome1. In a previous study, we analysed (close to) chromosome-level assemblies from six extant birds (and a lizard outgroup) to determine the most likely karyotype of the neornithine ancestor for the macrochromosomes and the neognathe ancestor for the microchromosomes2. Recreating the most parsimonious sequence of events that might have led to contemporary genome structures (karyotypes), we determined that chicken (Gallus gallus) was the closest karyotypically to the reconstructed ancestral pattern, with zebra finch (Taeniopygia guttata) and budgerigar (Melopsittacus undulatus) undergoing the most intra- and interchromosomal rearrangements, respectively. In the current study, to reconstruct the most likely karyotype of the diapsid common ancestor (DCA >255 mya), we applied similar approaches, i.e. the multiple-genome rearrangement and analysis (MGRA2) tool. We focussed on the best-quality chromosome-level assemblies of avian and reptilian genomes and a mammalian outgroup. Supplementing bioinformatic data with novel molecular cytogenetic approaches on turtle metaphases, we tested the hypothesis that the typical karyotype seen in neornithine birds underwent few interchromosomal rearrangements since the divergence of turtles from archosaurs (birds and crocodilians) <255 mya. Combining both sets of data, we thence inferred the most parsimonious sequence of events that occurred from the diapsid ancestor, to the archelosaur ancestor3, and thence via non-avian theropod dinosaurs to extant birds (see Supplementary Note 1 for divergence times).

kevin1981
2018-Aug-28, 01:16 AM
Scientists have not actually reconstructed 100 million year old Dinosaur genomes.

They have inferred from the evidence that they currently have that Dinosaur genomes were made up of many chromosomes. Even more than humans. Us Humans have 23 pairs of chromosomes in our genome. According to these Scientists, Dinosaur genomes had more..

And one of the main reasons why the Dinosaur species were so varied is down to having many chromosomes in there genome.

Jens
2018-Aug-28, 01:53 AM
Scientists have not actually reconstructed 100 million year old Dinosaur genomes.

They have inferred from the evidence that they currently have that Dinosaur genomes were made up of many chromosomes. Even more than humans. Us Humans have 23 pairs of chromosomes in our genome. According to these Scientists, Dinosaur genomes had more..


Lots of organisms have more than us. There's a kind of butterfly that has 450. :)

WaxRubiks
2018-Aug-28, 03:26 AM
plus they'd need an egg.

kevin1981
2018-Aug-28, 10:01 PM
Lots of organisms have more than us. There's a kind of butterfly that has 450. :)

Wow thats amazing ! How come it has so many chromosomes.. ? (I bet you knew i was going to ask that !) One would think that because it is such a small organism it would not need too many of them..

I am guessing here but maybe they are relatively short molecules so the organism needs more of them. Also, i guess the organism goes through different life cycle stages so maybe that has something to do with it as well ?

kevin1981
2018-Aug-28, 10:07 PM
plus they'd need an egg.


I know it is highly unlikely but if we managed to discover or replicate a Dinosaurs DNA, using todays technology, could we not replicate a suitable egg for the Dinosaur to fertilise in ?

Swift
2018-Aug-29, 08:42 PM
I know it is highly unlikely but if we managed to discover or replicate a Dinosaurs DNA, using todays technology, could we not replicate a suitable egg for the Dinosaur to fertilise in ?
I don't know, but I suspect that the egg is not the biggest problem. For example, people have talked about using an elephant egg (with the DNA removed) to recreate a wooly mammoth, and to gestate it in a female elephant. I suspect they could use either a bird egg or a reptile egg.

I have to admit I barely understood what they were talking about in the abstract or the article, but I don't think they have recreated the full DNA of a dinosaur, but have made projections (models) of what the overall structure of what the genome would have looked like (which I don't think is the same thing). Here is the sciencedaily (https://www.sciencedaily.com/releases/2018/05/180521092653.htm) take on it.


A discovery by scientists at the University of Kent has provided significant insight into the overall genome structure of dinosaurs.

By comparing the genomes of different species, chiefly birds and turtles, the Kent team were able to determine how the overall genome structure (i.e. the chromosomes) of many people's favourite dinosaur species -- like Velociraptor or Tyrannosaurus -- might have looked through a microscope.

The research was carried out in the laboratory of Professor Darren Griffin, of the University's School of Biosciences, and is now published in the journal Nature Communications. It involved extrapolating the likely genome structure of a shared common ancestor of birds and turtles that lived around 260 million years ago -- 20 million years before the dinosaurs first emerged.

Dr Becky O'Connor, senior postdoctoral researcher and co-author of the Nature Communications paper, then traced how chromosomes changed over evolutionary time from a reptile ancestor to the present day.

The team found that, although the individual chromosomes rearranged their genes internally, this did not occur much at all between the chromosomes -- what the scientists describe as 'a significant discovery'.

This is not the same as the complete DNA sequence of a dinosaur.

Roger E. Moore
2018-Sep-20, 07:21 PM
My bad. I should have said "extinct Pleistocene animals" instead of "dinosaurs". Apologies all around.

http://www.foxnews.com/science/2018/09/18/woolly-mammoths-will-roam-new-jurassic-park-style-theme-park-with-cave-lions-and-extinct-horses-in-ten-years-russian-scientists-say.html

10 years until Russia opens its "Jurassic park", says Fox News.

Copernicus
2018-Sep-21, 11:35 PM
My bad. I should have said "extinct Pleistocene animals" instead of "dinosaurs". Apologies all around.

http://www.foxnews.com/science/2018/09/18/woolly-mammoths-will-roam-new-jurassic-park-style-theme-park-with-cave-lions-and-extinct-horses-in-ten-years-russian-scientists-say.html

10 years until Russia opens its "Jurassic park", says Fox News.

I remember seeing articles like this, Russia cloning a mammoth, in my chemical engineering school walls at UW-Madison in 1983, along with projections that we would have clean nuclear fusion within 20 years. I also remember an old professor working on hydrogen fuel cells at that time. Thing is, I do believe all these things are 10 years away now. Of course we do have hydrogen fuel cells now. But they will be economically viable.

Roger E. Moore
2018-Sep-24, 03:56 PM
Looking online for more information on "Pleistocene Park", no having much luck.

Did, however, have a thought about the movie that could be made of it.... see image.

Roger E. Moore
2018-Sep-28, 01:50 PM
http://rsos.royalsocietypublishing.org/content/5/9/181295

With the renewed interest in the biggest-bird-ever moas (elephant birds), and given that we have a lot of their remains (recent DNA), let's ask a question: If it was possible to recreate moas using ostriches (for eggs), would that be a good idea? Keep in mind that they almost certainly cannot live in the wild, as their original habit has probably been converted to farmland or urban areas, so a zoo or wildlife park would be their only option for survival.

Would it hurt to bring dodos back as well, under the same conditions?

Roger E. Moore
2018-Sep-28, 02:44 PM
https://www.livescience.com/62359-dodo-murdered-shotgun.html

Also, a dodo murder case.

Relevant because extractable dodo DNA does exist.

============

LATE ADD: https://web.archive.org/web/20180909020311/https://www.smithsonianmag.com/science-nature/these-are-extinct-animals-we-can-should-resurrect-180954955/

"These Are the Extinct Animals We Can, and Should, Resurrect"
Biologist Beth Shapiro offers a guide to the science and ethics of using DNA for de-extinction.

Roger E. Moore
2018-Oct-01, 12:36 PM
I have a suspicion that in the zoos of the future, the animals and plants therein will more often be genetically engineered "designer" critters than "natural" ones. For one thing, there is a well-documented mass extinction underway, and we aren't going to have a lot of rhinos and gorillas and such. However, we might have designer giant flightless birds, not moas or elephant birds but giant two-legged birds resembling extinct Gastornises (Diatrymas). These might look amazingly like chocobos...

https://en.wikipedia.org/wiki/Chocobo

...or D&D game axebeaks...

https://www.google.com/search?q=axebeak&tbm=isch&tbo=u&source=univ&sa=X&ved=2ahUKEwjg4NGNoOXdAhWE0VMKHY2OB4AQsAR6BAgGEAE&biw=1920&bih=911

...or some other trademarked/copyrighted critter from gaming or fantasy/SF literature, and their genes will of course be patented. Imagine this line of reasoning extended ad infinitum.

Gorilla? What's a gorilla? The dragons from Game of Thrones and Lord of the Rings are in Pen Three.

Roger E. Moore
2018-Oct-01, 01:40 PM
I would go further and predict that you can have multiple patented versions of things like Tyrannosaurus Rex, because--supposing that Jurassic Park appeared and the creatures therein had part of their DNA synthesized (e.g., deriving part of their DNA from amphibians as in the original novel)--you could get variations on the synthesized DNA leading to variant T. rexes. This T. rex was made using a chicken's DNA, and this one a komodo dragon's DNA, etc. They mostly look the same with minor differences, but hey, a big dino is a big dino.

Russian zoos might have patented wooly mammoths, but Japanese zoos might have their own patented wooly mammoths, derived using different DNA strands from modern elephants producing much the same results. They used African elephants, we used Indian elephants, etc.

Would such a variety of weird designer critters lead to less interest in actual real critters like Siberian tigers and white rhinos, further endangering their existence as funding for regular zoos declines?

================

https://ghr.nlm.nih.gov/primer/testing/genepatents

U.S. National Library of Medicine: Can genes be patented?

A gene patent is the exclusive rights to a specific sequence of DNA (a gene) given by a government to the individual, organization, or corporation who claims to have first identified the gene. Once granted a gene patent, the holder of the patent dictates how the gene can be used, in both commercial settings, such as clinical genetic testing, and in noncommercial settings, including research, for 20 years from the date of the patent. Gene patents have often resulted in companies having sole ownership of genetic testing for patented genes.

On June 13, 2013, in the case of the Association for Molecular Pathology v. Myriad Genetics, Inc., the Supreme Court of the United States ruled that human genes cannot be patented in the U.S. because DNA is a "product of nature." The Court decided that because nothing new is created when discovering a gene, there is no intellectual property to protect, so patents cannot be granted. Prior to this ruling, more than 4,300 human genes were patented. The Supreme Court's decision invalidated those gene patents, making the genes accessible for research and for commercial genetic testing.

The Supreme Court's ruling did allow that DNA manipulated in a lab is eligible to be patented because DNA sequences altered by humans are not found in nature. The Court specifically mentioned the ability to patent a type of DNA known as complementary DNA (cDNA). This synthetic DNA is produced from the molecule that serves as the instructions for making proteins (called messenger RNA).

=============

Can nonhuman organisms be patented?

https://en.wikipedia.org/wiki/Diamond_v._Chakrabarty (yes, within limits)

https://en.wikipedia.org/wiki/Biological_patents_in_the_United_States (same)

Roger E. Moore
2018-Oct-01, 02:20 PM
CRISPR... is this how we get Jurassic Park? (or Pleistocene Park?)

http://www.nature.com/articles/s41467-018-04252-2

Full article from this June, overview of the CRISPR gene-editing system.

selden
2018-Oct-01, 02:46 PM
One possible scenario might be similar to that depicted in the Bladerunner movies, with people contracting for or purchasing synthetic organisms, perhaps as pets or ornaments, or perhaps for more serious applications. (Un)fortunately, I doubt it'll happen as soon as those movies suggest.

Swift
2018-Oct-01, 02:58 PM
I have a suspicion that in the zoos of the future, the animals and plants therein will more often be genetically engineered "designer" critters than "natural" ones. For one thing, there is a well-documented mass extinction underway, and we aren't going to have a lot of rhinos and gorillas and such.
I have the complete opposite prediction. Zoos are rapidly becoming our "Noah's ark", preserving animals that are going extinct in the wild (I do completely agree that we are in the middle of a a mass extinction event (https://en.wikipedia.org/wiki/Holocene_extinction)). They are entirely too busy with that, than to go about creating designer, imaginary animals, or long extinct ones.

But I also suspect that there will be attempts to either bring back extinct animals (mammoths being much more likely than T. Rex) or create designer animals like dragons. But I also expect they will more likely be in amusement parks and similar, rather than zoos.

Roger E. Moore
2018-Oct-01, 07:58 PM
I have the complete opposite prediction. Zoos are rapidly becoming our "Noah's ark", preserving animals that are going extinct in the wild (I do completely agree that we are in the middle of a a mass extinction event (https://en.wikipedia.org/wiki/Holocene_extinction)). They are entirely too busy with that, than to go about creating designer, imaginary animals, or long extinct ones.

But I also suspect that there will be attempts to either bring back extinct animals (mammoths being much more likely than T. Rex) or create designer animals like dragons. But I also expect they will more likely be in amusement parks and similar, rather than zoos.

I would hope you are right, but big money makes strange things happen.

Roger E. Moore
2019-Apr-01, 06:00 PM
Re-arguing the dinner scene in the first "Jurassic Park" movie: Was Jeff Goldblum's character right?

https://www.washingtonpost.com/lifestyle/magazine/would-bringing-back-extinct-animals-turn-out-as-badly-as-it-did-in-jurassic-park/2019/03/29/19688e90-4412-11e9-8aab-95b8d80a1e4f_story.html?utm_term=.d2771207c3d8

Would bringing back extinct animals turn out as badly as it did in ‘Jurassic Park’?
By Jason Nark, April 1 at 9:00 AM

On a frigid January night, a Harvard genetics professor with a billowing white beard stood stage left in a theater on Manhattan's Upper East Side, an icon of the environmentalist movement in a fleece vest beside him. Both men were staring down a toothy problem: How could they convince their counterparts on the stage, along with the 300 people who'd filed into Hunter College's Kaye Playhouse for a debate, that the world should bring back velociraptors or, at the very least, an extinct pigeon?

Noclevername
2019-Apr-10, 04:39 PM
http://www.foxnews.com/science/2018/09/18/woolly-mammoths-will-roam-new-jurassic-park-style-theme-park-with-cave-lions-and-extinct-horses-in-ten-years-russian-scientists-say.html

10 years until Russia opens its "Jurassic park", says Fox News.

Fox News is an entertainment channel. They did not meet the licensing standards for a registered Journalism outlet. So, not a valid citation source.

bknight
2019-Apr-10, 07:13 PM
Fox News is an entertainment channel. They did not meet the licensing standards for a registered Journalism outlet. So, not a valid citation source.

Who administers this licensing standard and what was Fox deficient?

Roger E. Moore
2019-Apr-10, 08:45 PM
Fox News is an entertainment channel. They did not meet the licensing standards for a registered Journalism outlet. So, not a valid citation source.

I once researched this charge, and it is not true. It spilled out of a case in which a Fox News station fired two reporters. I studied this event at length, but this is not the forum for a discussion. It gets very political. I'll leave it at that.

Noclevername
2019-Apr-10, 11:52 PM
I once researched this charge, and it is not true. It spilled out of a case in which a Fox News station fired two reporters. I studied this event at length, but this is not the forum for a discussion. It gets very political. I'll leave it at that.

Noted.