Evolution by geneticists again: yet another date for when polar bears arose

The latest addition to the never-ending story of when-and-why polar bear evolution took place according to geneticists (Liu et al. 2014 — the 8th such paper in less than 4 years, if you can believe it) is getting way, way more media attention than it deserves.

Lui et al. 2014 figure provided in the abstract.

Liu et al. 2014 figure provided in the abstract.

This multi-member research team used a new data set (mostly Scandinavian brown bears and Greenland polar bears, for a change) to add not much of anything new on the evolutionary insight front except yet another estimate of when polar bears came to be.1

However, the real focus of the paper is the description of their finding of a few genetic differences between brown bears and polar bears that they identified. They found a few genes in polar bears were different than brown bears and made a boat load of assumptions about what these might mean.

Their discovery was not accompanied by any attempt to demonstrate that the changes in gene architecture they found also involved a change in the function of the genes or were associated with different effects on bear physiology. If a changed gene cannot be shown to act differently or to have a demonstrated new physiological effect on the animal in question, the changes themselves mean next to nothing – especially for evolution!

That’s my take – see what you think. It looks long but a lot of it is quotes.

From ScienceDaily (May 8, 2014), about the authors:

The study was a collaboration between Danish researchers, led by Eske Willerslev and including Rune Dietz, Christian Sonne and Erik W. Born, who provided polar bear blood and tissue samples; and researchers at BGI in China, including Shiping Liu, Guojie Zhang and Jun Wang, who sequenced the genomes and analyzed the data together with a team of UC Berkeley researchers, including Eline Lorenzen, Matteo Fumagalli and Rasmus Nielsen. Nielsen is a UC Berkeley professor of integrative biology and of statistics.

Below are a number of eyebrow-raising quotes from the UC Berkeley press release, with my comments below each:

The genome analysis comes at a time when the polar bear population worldwide, estimated at between 20,000 and 25,000, is declining and its habitat, Arctic sea ice, is rapidly disappearing.”

SJC: Since there is nothing – not a single sentence – in the paper pushing a connection to the ‘polar bears are doomed due to declining sea ice‘ mantra (I was ever so pleasantly surprised to find), which makes this statement distinctly out of place in the press release. Whose idea was that – the university PR department? Or one of the Berkeley co-authors who couldn’t get the others to agree to having it in the paper?

And it isn’t true, as I’ve pointed out many times: the worldwide population of polar bears is not declining (it’s been stable for the last 30 years) and the sea ice habitat that’s critical to polar bears (spring through early summer ice) has declined a bit over the last 30 years but nothing to get bent out of shape about (i.e., within two standard deviations of the 30 year average), see previous post here.

“As the northern latitudes warm, the polar bear’s distant cousin, the brown or grizzly bear (Ursus arctos), is moving farther north and occasionally interbreeding with the polar bear (Ursus maritimus) to produce hybrids dubbed pizzlies.

SJC: Again? How many times do we have to go through this with geneticists? Interbreeding of polar bears with grizzlies has nothing whatsoever to do with Arctic warming and everything to do with the fact that tundra grizzly populations are increasing and male grizzlies wander long distances in the spring. See detailed discussion of the issue here.

Their ability to interbreed is a result of this very close relationship, Nielsen said, which is one-tenth the evolutionary distance between chimpanzees and humans. Previous estimates of the divergence time between polar bears and brown bears ranged from 600,000 to 5 million years ago. [Liu and colleagues estimate 343,000-479,000]

“It’s really surprising that the divergence time is so short. All the unique adaptations polar bears have to the arctic environment must have evolved in a very short amount of time,” he said. These adaptations include not only a change from brown to white fur and development of a sleeker body, but big physiological and metabolic changes as well. “There has been a lot of debate about it, but I think we really nailed down what the divergence time is between them, and it is surprisingly recent.” [my bold]

SJC: “Surprisingly recent” — as were three of the other estimates published within the last 4 years (two other were just a bit older, see list below).1 And of course, this group is really, really sure that this time, they’re the ones with the right answer and everyone before them has been wrong. That could be, but it could also be that the authors of the next study published (later this year perhaps?), will be just as sure about yet another estimate for when polar bears arose. Shall we start taking bets?

“What drove the evolution of polar bears is unclear, though the split from brown bears (dated at 343,000-479,000 years ago) coincides with a particularly warm 50,000-year interglacial period known as Marine Isotope Stage 11. Environmental shifts following climate changes could have encouraged brown bears to extend their range much farther north. When the warm interlude ended and a glacial cold period set in, a pocket of brown bears may have become isolated and forced to adapt rapidly to new conditions.” [my bold]

SJC: Are they serious? A simple expansion of their range — because there was more of the same habitat available — caused one group of brown bears to split genetically from other brown bears during a warm Interglacial, but it was the following cold Glacial that made some of the expanded group into polar bears?  Speculation is one thing, but this makes no sense.

Note, please, that none of these co-authors are general evolutionary biologists – again (see the last example here), we have geneticists plucking an evolutionary scenario out of the air to try and make their data sound vaguely plausible to people who don’t think about it too much. They don’t seem to care if it doesn’t make any biological sense or fit other kinds of evidence.

Polar bear female and her two cubs on the sea ice near Kap Tobin, Scoresby Sound, Central East Greenland (courtesy Rune Dietz, Aarhus University).

Polar bear female and her two cubs on the sea ice near Kap Tobin, Scoresby Sound, Central East Greenland, where some of the samples for this study were collected (provided by Rune Dietz, Aarhus University).

Nature News (May 8, 2014) carried the following story: Genome reveals polar bear’s youth: Analysis finds the animals diverged from brown bears less than 500,000 years ago”

Some quotes:

Charlotte Lindqvist, an evolutionary biologist at the University of Buffalo in New York, had previously estimated that polar bears emerged 4 million to 5 million years ago. “Our model was probably too simple,” she says. But she is sceptical that the split occurred as recently as Nielsen’s work suggests. “This estimate may be based on better models, but it is still highly impacted by assumptions,” she adds. “I don’t think we’re there yet.

Polar bears consume a high-fat diet of marine mammals, mostly ringed and bearded seals. Nielsen and his colleagues find that they may have adjusted to this diet in fewer than 20,500 generations, “an unprecedented timeframe for rapid evolution”, they write.” [my bold]

SJC: I critiqued the estimate Lindqvist mentions, 4-5 million years ago (published in Miller et al. 2012), here.  Odd that she doesn’t mention she was lead author on a similar paper published just a few years before that (Lindqvist et al. 2010) which gave an entirely different estimate (see list below).

And as for the “rapid” change business, I hate to burst their bubble: “20,500 generations” is only “an unprecedented timeframe for rapid evolution” if you’re a geneticist who assumes everything happens with glacial slowness because the only ‘evolution’ you know about is the genetic change component.

Biological evolution is a complex process and there is a lot we still don’t understand about how it works, but we do know that in many cases, new species have arisen in many, many fewer than 20,500 generations (which would be ~300,000 years for polar bears, using the out-of-date generation time of 15 years that the Polar Bear Specialist Group uses)!

There is a sizeable body of evidence for evolutionary change and adaptation taking place within only a few generations – I wrote a Ph.D. dissertation and a book on that topic. Explaining how and why it can happen so fast has still not been sorted out (I developed a set of testable hypotheses) but the evidence for very rapid change as an evolutionary fact is solid. Here (and here), is but one example: a 30-year study of Darwin’s finches on the Galapagos demonstrated rapid change in field studies that has been supported by genetic followup.

[order my book here and I’ll send an autographed copy; also available at Amazon.com in paperback, with an ebook available through Powell Books]

OK, let’s move on. It seems the journal Science also found this paper too compelling to miss: “Polar Bear Evolution Was Fast and Furious” (May 8, 2014). Some quotes and comments:

For polar bears, being tubby is a way of life. Fat can make up 50% of their body weight; the blubber-laden seals they eat make bacon look downright healthy. Now, a new, extensive comparison of the genomes of polar bears and their closest relative, the brown bear, has revealed how polar bears survive such unhealthy diets.

The work also suggests that the bears evolved these changes relatively quickly, likely because they had to adapt to extreme conditions that forced them to switch to a diet that would be toxic to other mammals. “It’s a schoolbook example of evolution,” says Eske Willerslev, an evolutionary geneticist at the University of Copenhagen who helped the lead the research.

In brown bears, the sequence of this gene [APOB, which helps transfer fat from blood into cells] varies from one bear to another, but all the polar bears surveyed have an identical version, with the exact same genetic code at nine variable spots in the gene, about half of which should change the function of the APOB protein.”

That all polar bears have the same version indicates that it is very beneficial, perhaps enabling the animals to eat lots of fat without developing artery-clogging plaques that can plague humans who eat high-fat diets, says study co-author Eline Lorenzen, a molecular ecologist at the University of California (UC), Berkeley. [my bold]

SJC:  “Unhealthy”? “Toxic”? Do these folks never open a book that’s not about genes? Have they never heard about the traditional high fat diets of the Inuit (who incidentally, also live in the Arctic)? I found this online: “The Inuit Paradox: How can people who gorge on fat and rarely see a vegetable be healthier than we are?” (Discover Magazine, October 2004), pdf here.

The emphasis on fat and cardiac function related genes in this paper is unfortunately another example of the no-news attention-seeking we’ve come to expect from geneticists lately. They simply cannot wait until they have something really significant to report before asking for massive public acknowledgement of their work via extensive media attention.

It’s one thing to publish a paper on another dull discovery – has to be done – but quite another to hype it up to be something it’s not. This paper got the hype in spades, courtesy an ever-compliant media unwilling to ask any critical questions (and, I suspect, a well-connected Berkeley PR department).

OK, I’m done — and not impressed. The paper is open access (see references below) if you want to wade through it yourself. Other links of interest as well.

Other media outlets that carried the story, many of which simply repeated parts of the press release:
“How do you survive a high-fat diet? Ask a polar bear” (Reuters, May 8, 2014)

“Scientists investigate why obesity is good for polar bears” (The Independent, UK, May 8, 2014). [which attributes the wrong journal for the paper]

“Polar Bears Evolved to Eat Fatty Foods Without Heart Harm” (Discover Magazine, May 8, 2014) – oh, the irony (see the article they published on Inuit diets mentioned above).

“If Polar Bears Can Eat A Ton Of Fat And Be Healthy, Why Can’t We?” (NPR, May 8, 2014).

“Polar bears could hold key to solving obesity crisis: Polar bears eat a high fat diet which would be disastrous for humans, so understanding their DNA could help the fight against obesity” (The Telegraph, UK, May 8, 2014).

Footnote 1.
Estimates of polar bear age over the last 4 years (there were also some before that), counting down from the most recent:
8. Liu et al. 2014              < 500 thousand years ago [this post]
7. Cronin et al. 2014        1.2 million years ago
6. Cahill et al. 2013        ~600 thousand years ago (“similar to Hailer et al. 2012”)
5. Miller et al. 2012         ~4-5 milliion years ago
4. Hailer et al. 2012        ~600 thousand years ago
3. Davison et al. 2011    ~160 thousand years ago
2. Edwards et al. 2011   ~120 thousand years ago
1. Lindqvist et al. 2010   ~134 thousand years ago

References
Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, et al. 2013. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genetics 9(3): e1003345. doi:10.1371/journal.pgen.1003345

Cronin, M.A., Rincon, G., Meredith, R.W., MacNeil, M.D., Islas-Trejo, A., Cánovas, A. and Medrano, J. F. 2014. Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences. Journal of Heredity, in press. http://jhered.oxfordjournals.org/content/early/2014/01/28/jhered.est133.abstract

Davison, J., Ho, S.Y.W., Bray, S.C., Korsten, M., Tammeleht, E., Hindrikson, M., Østbye, K., Østbye, E., Lauritzen, S-E., Austin, J., Cooper, A., & Saarma, U. 2011. Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species. Quaternary Science Reviews 30:418-430.

Edwards, C.J., Suchard, M.A., Lemey, P., Welch, J.J., Barnes, I., Fulton, T.L., Barnett, R., O’Connell, T.C., Coxon, P., Monoghan, N., Valdiosera, C.E., Lorenzen, E.D., Willerslev, E., Baryshnikov, G.F., Rambaut, A., Thomas, M.G., Bradley, D.G. and Shapiro, B. 2011. Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology 21:1251-1258.

Lindqvist, C., Schuster, S.C., Sun, Y., Talbot, S.L., Qi, J., Ratan, A., Tomsho, L., Kasson, L., Zeyl, E., Aars, J., Miller, W., Ingólfsson, Ó., Bachmann, L. and Wiig, Ø. 2010. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proceedings of the National Academy of Sciences USA 107:5053-5057. http://www.pnas.org/content/107/11/5053.full.pdf+html

Liu, Shiping, Eline D. Lorenzen, Matteo Fumagalli, Bo Li, Kelley Harris, Zijun Xiong, Long Zhou, Thorfinn Sand Korneliussen, Mehmet Somel, Courtney Babbitt, Greg Wray, Jianwen Li, Weiming He, Zhuo Wang, Wenjing Fu, Xueyan Xiang, Claire C. Morgan, Aoife Doherty, Mary J. O’Connell, James O. McInerney, Erik W. Born, Love Dalén, Rune Dietz, Ludovic Orlando, Christian Sonne, Guojie Zhang, Rasmus Nielsen, Eske Willerslev, Jun Wang. 2014. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157:785-794. Open access DOI: 10.1016/j.cell.2014.03.054 Pdf here.

Miller, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., Zhao, F., Kim, H.L., Burhans, R.C., Drautz, D.I., Wittekindt, N. E., Tomsho, L. P., Ibarra-Laclette, E., Herrera-Estrella, L., Peacock, E., Farley, S., Sage, G.K., Rode, K., Obbard, M., Montiel, R., Bachmann, L., Ingolfsson, O., Aars, J., Mailund, T., Wiig, O., Talbot, S.L., and Lindqvist, C. 2012. (in press). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences USA open access   Paper plus supplemental data

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