from the their-genes-should-have-worked-out-more dept.
Tasmanian tigers were suffering from poor genetic diversity prior to being hunted to extinction by humans:
Australian scientists sequenced the genome of the native marsupial, also known as the thylacine. It showed the species, alive until 1936, would have struggled to survive even without human contact. The research also provides further insights into the marsupial's unique appearance.
"Even if we hadn't hunted it to extinction, our analysis showed that the thylacine was in very poor [genetic] health," said lead researcher Dr Andrew Pask, from the University of Melbourne. "The population today would be very susceptible to diseases, and would not be very healthy."
He said problems with genetic diversity could be traced back as far as 70,000 years ago, when the population is thought to have suffered due to a climatic event.
The researchers sequenced the genome from a 106-year-old specimen held by Museums Victoria. They said their study, published in the journal Nature Ecology and Evolution, is one of the most complete genetic blueprints of an extinct species.
Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore (open, DOI: 10.1038/s41559-017-0417-y) (DX)
Related: Huge Population and Lack of Genetic Diversity Killed Off the Passenger Pigeon
Related Stories
Four billion passenger pigeons vanished. Their large population may have been what did them in
Four billion passenger pigeons once darkened the skies of North America, but by the end of the 19th century, they were all gone. Now, a new study reveals that the birds' large numbers are ironically what did them in. The pigeons evolved quickly, but in such a way to make them more vulnerable to hunting and other threats.
[...] In 2014, Wen-San Huang, an evolutionary biologist at National Taiwan Normal University (NTNU) in Taipei, and colleagues turned to DNA in an attempt to solve the mystery. Genetic material from four 19th century museum specimens revealed that the species had relatively low genetic diversity—meaning that most individuals were remarkably similar to each other—and that its numbers had fluctuated 1000-fold for millions of years. Hunting and habitat loss came during a time when the species was already declining, the team concluded, which pushed the birds over the edge.
But the new study lays the lion's share of the blame back on people. Beth Shapiro, a paleogenomicist at the University of California, Santa Cruz, and colleagues sequenced the complete genomes of two passenger pigeons, and analyzed the mitochondrial genomes—which reside in structures that power cells—of 41 individuals. The specimens came from throughout the bird's range. In addition, they reanalyzed data from Hung's group, and, for comparison, sequenced the bird's closest living relative, the band-tailed pigeon.
(Score: 2) by Grishnakh on Tuesday December 12 2017, @05:18PM (4 children)
Since they've sequenced the genome of this extinct and famous animal, they should figure out how to revive it, Jurassic Park-style. Even if it has to be kept in zoos, it'd still be interesting to see living examples.
(Score: 0) by Anonymous Coward on Tuesday December 12 2017, @07:11PM (3 children)
Why would you revive something which was a genetic dead-end? This would be like some sort of a sick genetic-socialism.
(Score: 3, Touché) by bob_super on Tuesday December 12 2017, @08:13PM
Have you ever seen a Pug ?
(Score: 2) by Grishnakh on Tuesday December 12 2017, @09:32PM (1 child)
Why not? Besides, the "dead-endedness" can be fixed by some more genetic engineering or cross breeding.
If you could bring back this and maybe a few other extinct animals, and keep them in zoos in habitats closely resembling those they used to live in, just imagine how many people would pay for a ticket to see that.
Plus, the research would be useful for improving other species genetically, such as humans which to me look like they're not in genetically great shape either. I could be biased though, since I'm American, so most of what I see around me are obese people, but from what I'm reading, obesity is an epidemic in most developed nations, so clearly humans desperately need genetic engineering to deal with that flaw. Given the huge number of obese Americans (a majority of the population), and the high likelihood that you yourself are American (given your writing and this site's demographics), you're probably genetically inferior in this way too, so you should be all in favor of genetic research.
(Score: -1, Flamebait) by Anonymous Coward on Tuesday December 12 2017, @10:53PM
Enough with the bullshit nationalist attacks.
Go fuck a head cow.
(Score: 3, Informative) by Immerman on Tuesday December 12 2017, @05:21PM (12 children)
Thylacines weren't hunted to extinction by "humans" in general, they were hunted to extinction specifically by Europeans.
Meanwhile, humans had already been living alongside them in Australia for at least 48,000 years, possibly as long as 65,000 years if recent archaeological discoveries are to be believed. Within the error bars of their "as far as 70,000 years ago estimate", I'd guess.
And while early Aborigines wouldn't have been shepherds (having migrated a few tens of thousands of years before the invention of herding), and thus not particularly driven to intentionally wipe out local predators, they were still a new and extremely effective invasive predator that the locals all had to compete with. I imagine that put a pretty serious strain on most every large land-dwelling predator on the continent - which at first glance seems to be only the thylacines, and possibly a huge (5+m) lizard. The largest remaining Australian predator is the spotted quoll, which weighs only a few pounds.
Not that humans are necessarily *always* to blame - but megafauna extinction does seem to have followed us everywhere we went as we spread across the planet.
(Score: 0) by Anonymous Coward on Tuesday December 12 2017, @07:13PM (5 children)
Genetically robust species can make a comeback.
Ones that lack that (like cheetahs) struggle. You could say that Thylacines were already ripe for extinction.
(Score: 2) by Immerman on Tuesday December 12 2017, @07:48PM (4 children)
Not quite. The "robustness" that's in question is diversity. The mere fact that a species has been driven close enough to extinction that it has to make a comeback, will likely deprive it of much of that diversity going forward. Given enough time to prosper, mutation will eventually reintroduce diversity, but that takes many tens of thousands of years. Cheetahs experienced such a bottleneck about 10,000 years ago, at the end of the last ice age, and still have very little diversity.
Something happened to the Thylacines about 70k years ago that similarly bottlenecked the population - the fact that humans arrived in approximately the same time period, coupled with the fact that megafauna extinctions have followed humans wherever we've gone, suggests that humans might be what happened to them, or at least prevented them from prospering during their recovery.
However, humans also seem to have gone through a bottleneck at about the same time - so it is quite possible that some climate changes were responsible. If that were the case though, you would expect to see several species that dwindled or went extinct at about the same time - predators rarely suffer so long as prey is plentiful.
(Score: 2) by Grishnakh on Tuesday December 12 2017, @09:34PM (1 child)
Genetically speaking, humans are also extremely non-diverse. By all rights, we should be going extinct. Unfortunately, we don't have any real predators.
(Score: 2) by takyon on Tuesday December 12 2017, @09:38PM
Anti-humanist spotted.
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by frojack on Wednesday December 13 2017, @05:29AM (1 child)
This is the second genetic diversity responsible for extinction article in as many months. Both exonerating human actions, if not explicitly then by inference. The passenger pidgon was the other.
Genetic diversity as an Extinction mechanism is a relatively new theory, one that some people are trying to push very hard lately for some reason.
I'm not sure I buy the assessment of lack of diversity or the perceived death sentence it is made out to be. Alligators and crocodiles have low diversity as well as limited ranges. They are among the longest extant species around.
No, you are mistaken. I've always had this sig.
(Score: 2) by Immerman on Wednesday December 13 2017, @02:50PM
I've got to agree it's not a death sentence, just an increased vulnerability. The thylacines managed to hang on 70,000 years after their genetic bottleneck, until Europeans came along and hunted them to extinction. For that matter humans bottlenecked at about the same time, with some estimates putting the global population at only ~2000 individuals.
It also strikes me that while diversity is a big advantage against disease, and a longer-term one in terms of evolutionary adaptation, both thylacines and pigeons were hunted to extinction over a very short period by the most efficient predator on the planet. No amount of diversity is likely to help against that.
(Score: 2) by PartTimeZombie on Tuesday December 12 2017, @07:44PM (5 children)
The arrival of humans in Australia seemed to have had a huge impact on the megafauna.
As usual Wikipedia has a good article [wikipedia.org]
The Marsupial lion [wikipedia.org] seems to have died out about 46,000 years ago, and I don't imagine anyone wanted a 130 kg ambush predator living near the camp, so that might explain that.
I'm guessing that some of the other huge marsupials were slow moving and a 3,000 kg [wikipedia.org] wombat would have fed the village for a fair while.
(Score: 2) by Immerman on Tuesday December 12 2017, @08:12PM (4 children)
Indeed, I referred to that article when looking for info. From what I can tell there was lots of megafauna, but very few megafauna *predators* prior to human's arrival, at least on land. The marsupial lion that you mention (which I somehow overlooked as being a thylacine), the giant monitor lizard Megalania, and the Quinkana terrestrial crocodiles. It seems like pretty much everything else went extinct long before humanity evolved, or was small enough to not directly compete with us (though there's always the possibility that they were delicious, or at least easy to find/kill)
(Score: 2) by PartTimeZombie on Tuesday December 12 2017, @10:00PM (3 children)
The Demon Duck of Doom [wikipedia.org] was what I was really looking for, but it lived about 15 million years ago, so did not predate humans, which is nice.
A 2.5 metre tall, 250 kg bird with a head bigger than a horse would not make a great neighbour, except the article says it is now thought to have been a herbivore. Kind of shoots the whole theory down really.
(Score: 2) by Immerman on Wednesday December 13 2017, @01:36AM (2 children)
Don't let a little herbivorousness discourage your mindplay. Deer are herbivorous, but have been documented to be quite willing to intentionally eat any birds careless enough to linger in reach. A quick burst of calories and protein is rarely ignored, even by animals not optimized for it.
And to something with a head the size of a horse, you'd probably make a toothsome snack.
(Score: 2) by PartTimeZombie on Wednesday December 13 2017, @02:23AM (1 child)
I may have phrased that badly, I meant it's head was bigger than a horses head, not the whole horse.
I have no doubt it would have had no problem defending itself if it had to, and plenty of birds defend their young, so yes, potentially very dangerous.
(Score: 2) by Immerman on Wednesday December 13 2017, @04:08AM
Less entertaining, but I still wouldn't want to be stuck alone with one that hadn't eaten in several days...
(Score: 3, Informative) by Arik on Tuesday December 12 2017, @06:03PM (5 children)
The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.
<text continues at link>
If laughter is the best medicine, who are the best doctors?
(Score: 2) by c0lo on Tuesday December 12 2017, @07:13PM (4 children)
I wonder... how did they infer poor genetic diversity by scanning the genome of one specimen.
https://www.youtube.com/watch?v=aoFiw2jMy-0 https://soylentnews.org/~MichaelDavidCrawford
(Score: 4, Funny) by takyon on Tuesday December 12 2017, @07:14PM (1 child)
The paper is entirely open access this time. Be the change you want to see in the world and RTFA lul.
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 3, Informative) by c0lo on Tuesday December 12 2017, @07:19PM
I can't. Sleepless night.
https://www.youtube.com/watch?v=aoFiw2jMy-0 https://soylentnews.org/~MichaelDavidCrawford
(Score: 2) by VLM on Tuesday December 12 2017, @08:46PM (1 child)
Awful EE analogy coming in... genetic code is noisier than the typical executable linux elf files we're used to and analysis of the degraded signals and noise in the code indicates if the code went thru weird filters in the past in addition to the usual white noise that accumulates over time. Made possible by the "modem" in genetic code being pretty good by 1970s standards but pretty inferior by 1990s standards so its possible to have raw genetic code containing encoded nonsense. From memory its not a 1:1 map either and you can have multiple chunks of code do the same protein synthesis.
Its a bad indicator for monotheism... if our genetic code system was created instead of evolved, it was definitely not one smart engineer with one unified clear design, but definitely a very large ANSI / ISO standards committee involved.
(Score: 2) by Arik on Wednesday December 13 2017, @04:40AM
First paragraph was good but this one not so much.
We don't fully understand it yet, so it's quite presumptious to declare it inferior.
It's possible that the 'noise' and 'junk' are there for reasons we don't yet fully understand. It's even possible one of them was to allow this sort of retrospective analysis.
If laughter is the best medicine, who are the best doctors?
(Score: 2) by requerdanos on Tuesday December 12 2017, @09:46PM (4 children)
I get that lead researcher Dr Andrew Pask, from the University of Melbourne, a totally smart guy who is better at this than I ever will be, says that the population was in bad shape anyway:
Here's where it gets fuzzy--he cites:
Okay, hold on a second there.
So, if they hadn't gone extinct from hunting, then they would have been so weak and sickly as to only live just fine for tens of thousands of years?
I'm no research scientist, but that sounds like pretty poor reasoning from where I sit. If they lived for seventy thousand years after the genetic problems set in, that sounds pretty darned robust to me in spite of said problems. I think maybe it was the hunting that did them in, full stop.
(Score: 2) by takyon on Tuesday December 12 2017, @09:49PM (3 children)
Forgot to add this to the article:
Huge Population and Lack of Genetic Diversity Killed Off the Passenger Pigeon [soylentnews.org]
Plenty of things get hunted or killed off by humans, sure. Lack of genetic diversity could be a factor that pushes populations over the edge and into extinction.
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by requerdanos on Wednesday December 13 2017, @01:08AM (2 children)
Quoting the first comment appearing on that pigeon story, attributed to Grishnakh (2831):
That encapsulates what I was trying to say pretty well.
(Score: 0) by Anonymous Coward on Wednesday December 13 2017, @10:18AM (1 child)
A little predation keeps population genetics in shape. Extinction results from abrupt changes, when bar is suddenly raised too high and entropy (mutations) rate can't keep up - a problem similar to cryptographic security.
So, I guess that geologic periods with explosion of species were probably periods of presence of additional sources of entropy - either radiation, or mutagen chemical agents, or retroviruses.
It seems like we should have had a nuclear war to pay our dues to the nature and introduce more diversity.
(Score: 2) by requerdanos on Wednesday December 13 2017, @05:25PM
Well, the 30km Chernobyl exclusion zone and wildlife preserve is one area where we are doing this, and the Pacific ocean off the coast of Japan near Fukushima is another. Perhaps outright war isn't necessary.