DNA links between Polynesians and South American Indians

DNA has proven a genetic link between Polynesia and South America, but who did the long distance voyaging? A study suggests that people from South America sailed to Rapa Nui (Easter Island) and back, but local historian Scott Hamilton suggests Polynesians are more likely to have sailed to South America and back.

New Scientist: Polynesians and Native Americans met 800 years ago after epic voyage

Polynesians and Native Americans met and had children together around AD 1200, according to a study of modern Polynesian peoples’ DNA. But the encounter didn’t take place on Rapa Nui (Easter Island), the island closest to South America, as has long been suggested. Instead, the Polynesians in question were from islands hundreds of kilometres further away.

The Pacific islands of Polynesia were some of the last places to be settled by humans. Beginning about 5000 years ago, people sailed east from South-East Asia into the Pacific, and found hundreds of islands including Samoa and the Marquesas. The easternmost island, Rapa Nui, was the last to be settled.

This story is supported by genetic, archaeological and linguistic evidence linking Polynesian people with South-East Asians. But some anthropologists have long argued that Polynesians might also have some Native American ancestry, pointing to other factors, such as crops.

“There is the sweet potato in Polynesia, even though it was domesticated in, and is native to, the Americas,” says Alexander Ioannidis at Stanford University in California. It has also been claimed that the famous statues on Rapa Nui resemble ancient Peruvian statues.

Geneticists have found evidence of Native American genes in Polynesian people, but the results are disputed. Now Ioannidis and his colleagues have sequenced the full genomes of 354 Polynesian people from 17 islands, as well as 453 Native Americans from 15 groups from the Pacific coast.

They found small amounts of Native American DNA in Polynesians from the eastern islands: not just Rapa Nui, but also the Palliser islands, the Marquesas and Mangareva. We don’t know exactly which islanders were the point of contact, says the team, but they were almost certainly from one of the more westerly of the group. Later settlers carried the genes to the easterly islands, including Rapa Nui.

The big question now is: who made the journey? Did Polynesians sail east to South America and back, or did Native Americans stray west? Either fits the data, says Ioannidis.

Also from Nature: Native South Americans were early inhabitants of Polynesia

The early peopling of Polynesia attracted worldwide interest in 1947, when the Norwegian explorer Thor Heyerdahl set sail on the Kon-Tiki expedition to test his migration theory. The crew left Peru on a wooden raft, and after 101 days and a voyage of more than 7,000 kilometres, they reached Polynesian shores, thus demonstrating the possibility of early travel from South America to these Pacific islands.

Heyerdahl challenged the scientific community’s view that evidence pointed instead to the peopling of Polynesia by people travelling east from Asia, and his idea that Polynesia was initially populated by South Americans was generally criticized by scholars.

The same scientific community nevertheless discussed cultural contacts between the two regions, because a South American plant, the sweet potato, has a long history of cultivation in eastern Polynesia. The idea that Polynesians voyaged to South America and introduced the plant on their return to Polynesia became the accepted explanation for this.

The DNA evidence.

A key discovery came from their analysis of people from Rapa Nui — a signature could be assigned to Native South American populations from northern coastal regions of South America, and this component was independent of other large historical, or more-recent, admixture events.

A surprising finding is that this signal was also identified in other eastern Polynesian populations, for example in populations in Mangareva, in North Marquesas and South Marquesas, and in Palliser in the Tuamotu Islands.

Figure 1

These other islands lie farther from South America than does Rapa Nui, although for people sailing from South America they are destinations that would be aided by favourable trade winds and currents.

The authors made the notable discovery that an initial admixture event between Native South Americans and Polynesians took place in eastern islands of Polynesia around AD 1150–1230. The exception to this South American admixture timeframe is Rapa Nui, which had a later admixture, dated to around AD 1380.

The earliest genetic signal of Native Southern Americans found by the authors in Polynesia was from people of the Southern Marquesas islands, and the authors argue that Colombians mixed with Polynesians there around AD 1150. This date is so early that it could even suggest South Americans reached there before Polynesians arrived, which would make Heyerdahl partly right if it were the case that South Americans first settled at least the area of eastern Polynesia that has signs of early admixture.

The authors also raise other possible contact scenarios: for example, that Polynesian populations made voyages to South America and then returned to Polynesia along with South American people, or that people returned to Polynesia who carried Native South American genetic heritage. Ioannidis et al. suggest that further genetic studies will be needed to address such alternative hypotheses.

Scott Hamilton supports the latter. Via twitter:

Heyerdahl claimed Polynesians came from the Americas, that they were ‘Red Indians in the Pacific’. An array of evidence shows that Polynesia was settled from the west rather than the east. But tantalising evidence of some Polynesian-American contacts persists.

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Researchers like NZ’s Lisa Matisoo-Smith have found Polynesian chicken bones in Chile. The kumara is South American. Coastal American peoples like the Mapuche & the Chumash have Polynesian-style aquatechnology & words to match. Now DNA evidence of a link’s turned up.

New Scientist magazine has reported on DNA testing done by a group of Mexican researchers. The tests found a small but significant amount of indigenous American DNA in Eastern Polynesian peoples. But the researchers & New Scientist seem to me to misinterpret their data.

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Without any explanation of their reasoning, the DNA scientists & New Scientist’s journalists claim that the new data proves that indigenous Americans sailed to Polynesia. It seems to me vastly more likely that Polynesians reached the Americas, & returned with Americans.

The reed boats South American peoples used on Lake Titicaca & other relatively gentle areas of water seem unsuited to the Pacific. & there is no trace of the influence of American aquatechnology on Polynesian cultures. By contast, Polynesian sewn plank canoes were Americanised.

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It seems to me that the genetic scientists are unaware of the research that Matisoo-Smith & others have amassed about Polynesian journeys to the Americas. DNA data is fascinating; but it still needs careful, historically informed interpretation. This book’s a place to start.

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As with just about all science, this is a work in progress.

 

Covid-19 genome mutations used for tracking

For those who wanted some science…

Genome sequencing has been used to identify mutations of the Covid-19 virus, and while there is no evidence any known mutations have changed the characteristics of Covid-19 yet, it has provided a useful way of tracking the spread of the virus.

This phylogeny tree from Nextstrain, with each shade representing a different country and each branch a separate mutation, shows how mutations tend to be linked to a specific geographic location. Each dot represents a genome from the GISAID database.

Newsroom – The NZ strains: How the virus got here

On average, the virus is thought to undergo about 23.92 mutations a year, or two every month. This figure can help us backdate its emergence. If there is an average of 10 mutations from the supposed index case, then the virus likely entered the human population around five months ago – or early December.

Even the two most divergent strains have just 35 mutations, representing about 0.12 percent of the genome. By comparison, SARS, which is significantly deadlier but still very similar to Covid-19, is 21 percent distinct from SARS-CoV-2.

While the mutations may not make the virus more deadly or more transmissible, understanding where in the virus these mutations occur could help with efforts to create an antiviral medication.

One interesting example, in March a father and son arrived in New Zealand from the US and both tested positive, but they had different mutations that made it extremely unlikely they caught the virus from the same source.

“A Wellington man in his 30s and his father in his 70s have tested positive on their return from the United States. The man in his 30s became unwell on the flight and his father became unwell the day after they arrived,” Bloomfield said.

These two men, however, did not infect one another. Instead, they were likely infected in separate circumstances, each with one of the two strains detailed above. One of the viruses had five mutations that the other did not, making it extremely unlikely that one man had infected the other.”

Here the ESR has now sequenced 171 of the more than 600 cases referred to them, and has just received a new sequencer that wil double their testing capacity to 100 genomes a week. Their aim is to sequence all New Zealand cases.

This map charts the progress of the strains that made up the eight New Zealand cases on Nextstrain.

Our aim is to sequence every positive case in New Zealand,” Geoghegan said.

“Fortunately, that seems like a very realistic goal because we haven’t had that many cases. We’re in a really unique position to be able to do that. That will really provide us with an amazing dataset and a great case study, especially for international collaborations, to be able to understand how the virus spread here, what happened after we closed our borders, what happened after we went into Level 4 lockdown and as we begin to lift those lockdown restrictions, what happens to the transmission of the virus?”

Since New Zealand is a closed population, such studies could help researchers understand how the virus changes, without having to deal with the pressures of managing an active outbreak.

For example, an examination of different clusters in New Zealand could show cluster-specific mutations, allowing health officials to link closed cases with unknown origins to where they came from. Similarly, if a new case emerges out of nowhere, sequencing the genome of the patient’s virus could link it to another extant case or, through ruling out genomic connections to any of New Zealand’s cases, declare it an imported case.

A lengthy article but worth reading in you like a bit more depth and more science.

It’s incredible how science is now capable of sequencing RNA like this (as they do with DNA).

A bit more science: DNA vs. RNA – 5 Key Differences and Comparison

Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) are perhaps the most important molecules in cell biology, responsible for the storage and reading of genetic information that underpins all life. They are both linear polymers, consisting of sugars, phosphates and bases, but there are some key differences which separate the two. These distinctions enable the two molecules to work together and fulfil their essential roles. Here, we look at 5 key differences between DNA and RNA.

DNA vs. RNA – 5 Key Differences and Comparison

Jawbone from Tibet identified as Denisovan

Denisovans are an extinct human group similar to Neanderthals. Traces of both can be found in modern human genes, so interbreeding took place.

ABC (2016): Aboriginal Australians, Pacific Islanders carry DNA of unknown human species, research analysis suggests

They found Europeans and Chinese people carry about 2.8 per cent of Neanderthal DNA.

But Europeans have no Denisovan ancestry, and Chinese people only have 0.1 per cent.

Modern populations from South Pacific regions including Vanuatu, the Solomon Islands, Fiji, Papua New Guinea, New Caledonia, West Papua, and the Maluku Islands have 2.74 per cent of their DNA as coming from Neanderthals.

Mr Bohlender estimates the amount of Denisovan DNA in these people is as low as about 1.11 per cent, not the 3 to 6 per cent estimated by other researchers.

Therefore, Mr Bohlender and his colleagues came to the conclusion that a third group of hominids may have bred with the ancestors of Melanesians.

“The sequencing of complete Neanderthal and Denisovan genomes has provided several insights into human history. One important insight stems from the observation that modern non-Africans and archaic populations share more derived alleles than they should if there was no admixture between them. We now know that the ancestors of modern non-Africans met, and introgressed with, Neanderthals and Denisovans.”

Until recently the only identified Denisovan remains had been found in Siberia.

The Denisovans or Denisova hominins are an extinct species or subspecies of archaic humans in the genus Homo. Pending its taxonomic status, it currently carries temporary species or subspecies names Homo denisova,[1] Homo altaiensis, Homo sapiens denisova, or Homo sp. Altai. In 2010, scientists announced the discovery of an undated finger bone fragment of a juvenile female found in the Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans.

The lineage that developed into Denisovans and Neanderthals is estimated to have separated from the lineage that developed into “anatomically modern” Homo sapiens approximately 600,000 to 744,000 years ago. Denisovans and Neanderthals then significantly diverged from each other genetically a mere 300 generations after that. Several types of humans, including Denisovans, Neanderthals and related hybrids, may have each dwelt in the Denisova Cave in Siberia over thousands of years, but it is unclear whether they ever co-habitated in the cave. Denisovans may have interbred with modern humans in New Guinea as recently as 15,000 years ago.

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

Now what is believed to be a jawbone, found  found in a cave in Tibet in 1980, has been identified as Denisovan.

Stuff:  Ancient humans were more resourceful than we give them credit for

Scientists are being urged to step up the search for ancient human remains in Oceania and Asia, after researchers revealed a 160,000-year-old jawbone found in Tibet is from the archaic human Denisovan group.

Previously Denisovans – an extinct sister group of Neanderthals – were only known from a small collection of fossil fragments found in 2010 at Denisova Cave in Siberia.

Researchers have now identified the lower jawbone – found on the Tibetan Plateau in Baishiya Karst Cave in Xiahe, China in 1980 by a local monk – as being from a population closely related to the Siberian Denisovans.

“The Xiahe mandible likely represents the earliest hominin fossil on the Tibetan Plateau,” researcher Fahu Chen, director of the Institute of Tibetan Research, Chinese Academy of Sciences, said.

These people had already adapted to living in this high-altitude low-oxygen environment long before Homo sapiens even arrived in the region.”

Unless they find other remains that show otherwise.

Murray Cox, associate professor of computational biology at Massey University, said it used to be thought only modern humans could live on the Tibetan Plateau, and only from about 30,000 years ago.

“There’s a strong bias in much of our thinking – we tend to believe that only modern humans are clever enough to go to certain places or live in certain ways. It’s now clear we’ve overestimated our uniqueness. Archaic humans like Denisovans were much more resourceful and adaptable than we have given them credit for,” Cox said.

Perhaps most important was the finding that human remains misclassified in the 1980s were now being recognised as Denisovan

“This suggests that other Denisovan bones and remains are hiding in plain sight – sitting in museums and university collections around the world  – and we just need to put the correct label on them to get a better idea of what Denisovans looked like. This study is the first, probably of many, that I expect will find them,” Cox said.

Otago Palaeogenetics Laboratory director Nic Rawlence said Denisovans had left a genetic legacy within the genomes of east Asian, Aboriginal Australians and Melanesians through interbreeding.

“The genes that allow modern day Tibetans to survive at high altitudes can be traced back to interbreeding between Denisovans and the ancestors of Tibetans,” Rawlence, a senior lecturer in ancient DNA at the University of Otago, said.

“Until now this has always intrigued scientists as there was no evidence of Denisovans in central east Asia, and modern humans only arrived on the scene around 30,000-40,000 years ago.

“The 160,000-year-old Tibetan Denisovan goes someway to potentially explaining where and when this interbreeding occurred.” But the jury was still out on whether Denisovans were adapted to living at high altitudes. It may be that the genes involved were initially used for something else, then repurposed for surviving at high altitudes.

Research on this is obviously ongoing.

 

DNA nails historic offender

DNA has solved a twenty year old offence. It turns out to be a repeat offender – as often seems to be the case in sexual offences.

NZ wrestler Devon Bond admits 1994 rape after DNA hit

Former New Zealand representative wrestler Devon Charles Bond has admitted the horrific 1994 rape of a Christchurch woman, after a cold case DNA match.

Bond, 49, pleaded guilty on Monday in the High Court at Christchurch, on the morning his jury trial was due to begin.

The Crown will ask the court to consider an open-ended preventive detention sentence because Bond has a 1995 conviction for abducting a woman he put into the boot of his car.

It’s good to see DNA evidence helping solve historic offences. I hope it continues to nail repeat sexual offenders.

What has become apparent with sexual offending is that there seems to be a relatively small number of men who have been usually getting away multiple offences.

Obviously this has been bad, very bad, for the mostly female victims.

It’s also been a bad look for men in general, with some claims suggesting that sexual assaults have been perpetuated by an alarming number of men.

I’d like to see analysis of statistics on this, but I suspect that a relatively small proportion of men are responsible for the majority of assaults, especially those that are at the more serious send end of the scale.

Editing DNA

A technique called CRISPR (Clustered regularly-interspaced short palindromic repeats) has been developed that allows scientists to edit DNA – in particular to cut out bits so that the changes will be passed on through generations.

The Week: The genetic breakthrough that could change humanity, explained

What is CRISPR?
It’s a revolutionary gene-editing technique that enables scientists to snip out a piece of any organism’s DNA cheaply, quickly, and precisely — cutting and editing the code of life the way a film editor would splice an old film reel.

In creating CRISPR, scientists learned to use Cas9 to cut out a target gene within any cell, replace it with another gene if needed, and neatly stitch the ends of the DNA back together.

As a result, genetic research is nearing a breakthrough that could transform the world.

It’s already being used…

… to make certain crops invulnerable to killer fungi, and scientists have also created a strain of mosquitoes with malaria-blocking genes that the insects successfully passed on to 99.5 percent of their offspring.

It could be used to change humankind.

But the technique’s most promising application is as a potential cure for hereditary diseases. In theory, scientists could use CRISPR to cure single-gene defects like Huntington’s by editing out the disease-carrying gene from the DNA of a fetus in the womb — permanently erasing the disease from the person’s germ line, so the offspring would also be saved.

Apart from the logistics of editing the DNA of sufficient numbers of fetuses to make a significant difference there are possible serious drawbacks.

A team at Sun Yat-sen University in Guangzhou attempted to modify the germ line in dozens of human embryos, hoping to snip out a defective gene that causes a deadly blood disorder.

The study caused shock waves in the scientific community — but also highlighted the practical difficulties of DNA editing in higher organisms.

Of the 86 embryos used — all of which were nonviable — just four manifested the new gene designed to replace the defective one.

Worse, there were inexplicable mutations in genes that weren’t targeted by the researchers. “The number of unintended effects is precisely why this technique is not appropriate for use in clinical applications,” bioethics professor R. Alta Charo told Wired.

So it could result in worse problems than it is intended to solve. And these problems might not become apparent for some time – a generation or more.

And then there’s the issue of whether it could lead to fiddling with human characteristics.

The larger question, of course, is whether scientists should be tinkering with the human gene pool at all.

At some point, researchers could switch their attention from curing hereditary diseases to editing supposedly desirable traits into a person’s DNA, such as high intelligence, tall stature, or blue eyes.

“Great things can be done with the power of technology — and there are things you would not want done,” said Jennifer Doudna, a Berkeley biologist who co-invented CRISPR. “Most of the public does not appreciate what is coming.”

We have already seen what can happen when people have their appearance changed using poisons and plastic surgery. You can end up with anything between bland and the ridiculous.

It can remove the humanness from once human faces. But at least the physical characteristics won’t be passed on to the next generation (although too much money and too little sense could be).

DNA editing has much wider and deeper implications – but not for me, it won’t affect my generation.

More on CRISPR at Wikipedia.

Asians may be more Neanderthal than Europeans

Additional DNA knowledge on how much Neanderthal genes are mixed with human DNA has led to a new theory – that Asians have had a double dose of Neanderthal DNA, possibly at different times.

It’s interesting but is a developing party of evolutionary science and seems to disprove the last theory on the amount of Neanderthal DNA shared by us humans. And another recent study suggests otherwise. Never mind.

The key stages from A New Theory on How Neanderthal DNA Spread in Asia

  • Scientists estimate that the Neanderthals’ ancestors diverged from ours 600,000 years ago.
  • Neanderthals first appeared in Europe at least 300,000 years ago.
  • The oldest fossils of Neanderthals date back about 200,000 years, while the most recent are an estimated 40,000 years old. Researchers have found Neanderthal bones at sites across Europe and western Asia, from Spain to Siberia.
  • Our own ancestors remained in Africa until about 60,000 years ago, then expanded across the rest of the Old World.
  • About 50,000 years ago, Neanderthals interbred with the ancestors of living Europeans and Asians.
  • People who are not of African descent have stretches of genetic material almost identical to Neanderthal DNA, comprising about 2 percent of their entire genomes. These DNA fragments are the evidence that Neanderthals interbred with the early migrants out of Africa, likely in western Asia
  • People in China, Japan and other East Asian countries have about 20 percent more Neanderthal DNA than do Europeans.

The new theory:

But there are still uncertainties.

If Neanderthals became extinct 40,000 years ago, they may have disappeared before Europeans and Asian populations genetically diverged. How could there have been Neanderthals left to interbreed with Asians a second time?

It is conceivable that the extinction of the Neanderthals happened later in Asia. If that is true, there might yet be more recent Neanderthal fossils waiting to be discovered there.

Or perhaps Asians interbred with some other group of humans that had interbred with Neanderthals and carried much of their DNA. Later, that group disappeared.

Regardless of the finer details this is what they think some of your ancestors may have looked like.

Reconstruction of the head of the Shanidar 1 fossil, a Neanderthal male
who lived c. 70,000 years ago (John Gurche2010).
http://en.wikipedia.org/wiki/Neanderthal

But that’s just one interesting article and one handsome dude.

Another recent article citing DNA research claims there was no interbreeding with Neanderthals – The Neanderthal murder mystery.

Those scientists may not fancy being related to the this dep;iction of them:

Neanderthal