Neanderthal Genes, New Flu, Obamacare Agonistes

 

Were Neanderthals a Different Species?

It’s no longer news that everybody except (most? some? SEE FOOTNOTE) Africans possesses a bit of Neanderthal DNA. And it really is just a bit; the latest two studies, published just last week and drawn from the 1000 Genomes Project databank, put the average at less than 2 percent.

It turns out, though, that your 2 percent is likely somewhat different from my 2 percent. Adding up the disparate bits means that Neanderthals have contributed at least 20 percent of their genomes to anatomically modern humans. (“Anatomically modern humans,” that’s us, the last Homo standing, and for clarity and convenience, occasionally I will use the shorthand designation some paleontologists use:  AMH.)

The Neanderthal DNA scattered around the billions of modern human genomes could total as much as 40 percent or more of the Neanderthal genome, the researchers say. That means it might not always be necessary to raid precious fossils for their DNA or go through contortions to assemble error-free ancient DNA sequences and prevent contamination by modern DNA. It might be possible to do fossil-free studies of the Neanderthal genome, studies carried out on their DNA carefully preserved for science in billions of today’s human genomes.

We AMHs, it appears, are walking labs for the study of paleogenomics.

 

How Neanderthal DNA helped us

A portion of that legacy DNA seems to have done us good. About 3 in 5 of the AMH genomes from the 1000 Genomes Project that were examined in these two studies possess the Neanderthal versions of some DNA involved in making skin and hair. The researchers believe that may have helped our migrating ancestors adapt to a Northern climate, one that was colder and less sunny than their original home in Africa. It may also have bolstered our defenses against new pathogens.

But there are also big stretches of the AMH genome that contain no Neanderthal DNA at all. “To me, these ‘holes of Neanderthal sequence’ are the most interesting aspect,” Joshua Akey told me in an email. (Akey, who is at the University of Washington, is an author of one of last week’s papers, which appeared in Science. )”[T]hey might provide a roadmap to positions in the genome that endow uniquely human traits.”

Where they are absent, natural selection may have decided that the AMH versions were doing a better job and so eliminated the Neanderthal counterparts. Hence these “deserts” may help define the most important genetic differences between us and them.

 

Credit: Neanderthal Museum (Mettmann, Germany)

Credit: Neanderthal Museum (Mettmann, Germany)

What the DNA “deserts” mean

There are deserts on the X chromosome and in genes involved in the testes. Patterns like these in other species ranging from rabbits to fruit flies are regarded as signs that one species is about to split into two.

Hybrid males descended from both branches tend to be infertile, like mules. That’s because males have only one X chromosome, and if it happens to be one that impairs their fertility, then they may not reproduce. Females have two X chromosomes, so even if one is impaired, if the other one is normal, it can rescue her ability to bear young.

“So this suggests that the male hybrids might not have been fertile, whereas the females might have been fully fertile,” Svante Pääbo told Richard Harris of National Public Radio. Pääbo, the grand old man of ancient DNA based at the Max Planck Institute for Evolutionary Anthropology in Leipzig, was an author of the other paper, which appeared in Nature. We might have inherited most of our Neanderthal genes through hybrid females, he said. Fox News quoted Pääbo as saying Neanderthals must have been disappointed in their sons.

Another author, David Reich of Harvard Medical School, told reporters that we and Neanderthals “were at the edge of biological compatibility.”

“This underlines that modern humans and Neanderthals are indeed different species,” Fred Spoor told New Scientist. Spoor is also at the Leipzig Max Planck but was not a part of the Neanderthal research. Other scientists are more cautious about making so firm a declaration, but it’s clear that many lean toward that same conclusion, that Neanderthals were not Homo sapiens neanderthalensis but, rather, Homo neanderthalensis.

Darren Curnoe, a human evolutionary biologist at the University of New South Wales, blogged, “The latest findings from genome comparisons reinforce the status of Neanderthals and modern humans as distinct species. Those anthropologists who continue to regard Neanderthals as members of Homo sapiens now face a stronger challenge than ever reconciling their position with the DNA.”

 

Speak up

If there is one trait above all others that is responsible for our success, it is fluent language. That’s why a detail almost buried in the Science paper caught my eye, and a few other writers mentioned it in passing. The authors reported that none of the modern genomes they examined contained the Neanderthal version of the chromosome region where the FOXP2 gene is situated. In these 665 people, that region, on the long arm of chromosome 7, was one of those Neanderthal deserts.

All land vertebrates possess a version of this gene. One type of FOXP2 has been shown to be associated with vocal learning in young songbirds. More than a decade ago, researchers linked a mutant version of the human gene with a set of unusual language difficulties in a particular family.

Despite what you may have heard, FOXP2 is not a “language gene” per se. Among other functions, Andrea Andriadis said in a SciAm guest blog, it seems to affect motor neuron control in parts of the brain involved in the ability to vocalize.

In 2011, Pääbo reported that the modern human and Neanderthal FOXP2 genes were identical, according to Carl Zimmer at The Loom. This led to excited speculation that Neanderthals could probably speak as we do. But last year researchers discovered differences in the way the AMH and Neanderthal FOXP2 genes are regulated. The protein-coding sequences may be the same, but they are controlled in different ways.

The fact that none of the contemporary genomes studied seem to possess exactly the same version of FOXP2 as Neanderthals after all, that it looks as if none of the 665 people examined has hung on to the Neanderthal version, suggests that we may have found it wanting and evolution eliminated it entirely from our line. Which suggests, in turn, that Neanderthals might not have had our fluent speaking abilities after all.

(Please note that I’m just running my mouth here in the usual speculative Homo sap fashion, and that we are speaking of data from only 665 people; the Neanderthal capacity for speech has not been established either way.)

But since no evolutionary development has been more important to the rise of anatomically modern humans and our domination of the planet than language, it might perhaps be said that fluent speech by itself is a defining characteristic of our species.

And that hominins that lack it are not us.

 

Here’s the footnote mentioned in the first graf above

Africans may no longer be an exception to the Neanderthal intromission. It appears that Europeans and/or Eurasians went back to Africa a few thousand years ago. As is the human wont, they deposited DNA hither and thither, and some of it could have been tidbits of the Neanderthal DNA they carried.

This news grows out of a new paper showing that the Khoisan people, the click-speaking pastoralists of southern Africa, have some Eurasian DNA (up to 14 percent of the genomes in one population), and they got it between 900-1800 years ago.  This looks to have been the result of matings between Africans and Eurasians in East Africa about 3000 years ago. Another study reports a Neanderthal signal in the Yoruba.

In New Scientist, Catherine Brahic speculates that this means Neanderthal DNA may actually be widespread in Africa, courtesy of European carriers.  She quotes study author David Reich of Harvard thus: “I actually am not sure there’s any population that doesn’t have west Eurasian [DNA].”  He means DNA acquired in olden times, not the many cross-cultural “exchanges” of the last few hundred years.

 

Obamacare Agonistes

Obamacare has been having a very bad week, thanks to a new report from the Congressional Budget Office. The bad week is due partly to misinterpretations of the report’s conclusions, even by some very respectable media.  The misinterpretations have been trumpeted by enemies of this infant remodel of the US health care system, who capered with joy at this gift.  And it can be said that even correct interpretations of the data can be disconcerting in their potential implications.

The misinterpretation was that Obamacare (aka ACA) is going to cost 2 million jobs. But the report didn’t say that. It predicted that the labor force would be reduced by 2 million, quite a different matter.  Specifically, it said the ACA provides incentives for 2 million people to leave full-time employment by 2024. Some people will stop working jobs they have been hanging on to for the medical insurance. Others will abandon low-paying jobs in order to qualify for larger insurance subsidies. Keith Hennessey argues at length that the generous subsidies will trap low-income people and prevent them from climbing into the middle class.

Eric Wemple’s blog at the Washington  Post recounted how a number of publications had to revise their headlines,  including the Wall Street Journal, Politico, Forbes, and the Washington Post itsownself, which declared that Obamacare would result in 2 million fewer jobs.  (The revision said Obamacare would result in 2 million fewer workers.)   The National Review stuck with The CBO Just Nuked Obamacare.  A reasonable choice.  No incorrect specifics to revise, and I suppose it might even turn out to be accurate.  Horrors.

At Wonkblog, Sarah Kliff delves into specifics of the CBO report.  It concludes, she says, that the much-decried “insurance company bailout” will actually save money, but because of the botched rollout and web site nightmares of last fall (not yet entirely eliminated), 2 million fewer people than expected will enroll. In a different post, she sorts out details of research that helped the CBO arrive at its employment projections.

Paul Krugman disagrees with Kliff about insurance enrollment projections, and reproduces a CBO table to prove it.  He says, “Oh noes! The exchanges will cover 6 million people, not the 7 million we expected! The number of uninsured will fall 13 million, not 14 million!

“In short, CBO thinks that reform has been only mildly set back by the healthcare.gov mess, that at this point it’s going pretty well. And by the way, these are predictions we’ll be able to test in real time, unlike the labor force estimates, which will get lost in statistical noise.”

 

The influence of influenza

The new H10N8 bird flu virus killed an elderly Chinese lady in November, Karen Kaplan tells us at the LA Times’s Science Now. That’s the first death reported from H10N8, and there’s no evidence yet of person-to-person transmission. H10N8 has two mutations that seem to make it particularly virulent in mammals.

H7N9 flu data from last April. Deaths now number 300, a quarter of them fatal.

H7N9 flu data from last April. Deaths now number 300, a quarter of them fatal.

Meanwhile, the H7N9 no-longer-just-bird flu is rocketing along,  although  according to a just-published paper in the New England Journal of Medicine, person-to-person transmission has yet to be established.  Some 300 Chinese cases are now reported, about a quarter of them fatal. That’s a big and worrisome increase.  At ViroBlogy, Ed Rybicki asks, “So THIS is the next one?  Possibly?”

He’s happy a vaccine is in the works. Me too.

Judy Stone brings helpful clarity to her post all about flu at Molecules and Medicine. She sorts out the nomenclature, the history, and the prospects.  Excellent background.

 

Department of Self-Interest

The Neanderthal post above appeared in a somewhat different form last Tuesday at the Genetic Literacy Project, where I am a weekly columnist.  New posts on Tuesdays.  You can see my past posts here.  Along with some original contributions like mine, the Genetic Literacy Project (“Where Science Trumps Ideology”)  is an aggregation of genetics news with an emphasis on human and agricultural applications.  The aggregators are not digital, I am happy to report, but members of our very own species, AMH. They are adept at digging out a wide range of material, a lot of it from specialized nontechnical sources that will be new to you.

 

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2 Responses to Neanderthal Genes, New Flu, Obamacare Agonistes

  1. Doug says:

    One fascinating point if Dr Manica is correct sooner than later in here theory that Neanderthal DNA is ancestral DNA because there were many groups of AMA in Africa with varying degrees of connection to Neanderthal ancestry, then it may be inferred that the African group continued speciation in the circumstance that influenced adaptation into AMA. A more completely finished speciation, absent of the things we found to be on their way out in Europeans and Asians through Akey’s research, could be equated, by some, with Africans being more evolved. Maybe that is why we are getting this crammed down our throats the last 2 months and a strange no-mention of the other key articles. The ones who got excited about the big sex scandal that didn’t happen might be plenty consoled with this one. I am not black but somehow this makes me feel proud of my African friends knowing how we all take such delight in things rich, cool and often unique to them. Is it racist to say that? Might help the world to know if this were true; might not.

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  2. Doug says:

    Great Job on compiling so many important articles and yours is the most informative yet. Also glad you did not keep hammering in the idea of hybridization with Neanderthal and instead focused mainly on what we know. Your email buddy from Washington State, Joshua Akey provided the crowning jewel on all these Neanderthal genome based articles that started last year with Dr Svante Paabo great genome work. Two important articles that are missing in this incredible compilation, two that I hope you consider adding or asking Joshua Akey to give his thoughts on, are two research works published in PNAS last year that may provide an explanation why this pattern of slight dispersal of Neanderthal DNA in Africa and these large holes of active DNA that indicate hybrids would have had a hard time surviving.
    Dr Andrea Manica led a study at Cambridge University that was in response to Paabo’s interbreeding theory. She said,”Our work shows clearly that the patterns currently seen in the Neanderthal genome are not exceptional, and are in line with our expectations of what we would see without hybridization.”
    The other – Many University participated at the Department of Prehistory and Archaeology at the Spanish National Distance Education University (UNED) They used “ultrafiltration” to clean carbon contaminants that interfered with proper radio carbon dating which revealed that the extinction of Neanderthal happened much earlier, at 50,000 years ago while modern humans arrival in the Europe is still locked in at 42,000 years ago, even with the jawbone in the UK. That’s an 8,000 year gap and even considering the widest possible margin of error on all the measure, its a long way to any overlap time for mating. All good science considering your friend, Akey, possible would not have gone looking for Neanderthal in living humans if he knew we didn’t interbred. Wow, good thing he did!

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