There are a couple of interesting whale stories in the news today.

For nearly nine years Cornell University researcher Christopher Clark -- together with former U.S. Navy acoustics experts Chuck Gagnon and Paula Loveday -- has been trying to answer these questions by listening to whale songs and calls in the North Atlantic using the navy's antisubmarine listening system. Instead of being used to track Soviet subs as they move through the Atlantic, the underwater microphones of the Sound Surveillance System (SOSUS) can track singing blue, fin, humpback and minke whales.

From the acoustical maps he and his colleagues have obtained, Clark has come to realize that he has been thinking about whales at the wrong time scale. "There is a time delay in the water, and the response times for their communication are not the same as ours. Suddenly you realize that their behavior is defined not by my scale, or any other whale researcher's scale, but by a whale's sense of scale -- ocean-basin sized," he says.

Fuller version here.

Whalemeat samples bought from a Japanese sushi market and analysed by scientists indicate that experts have seriously underestimated the size of the populations that roamed the seas before industrial-scale hunting began more than a century ago. The numbers of some species may have been 10 times greater than previously calculated.

Fuller version here.
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ok, ok, brace yersel... yer hay'in a whale o a time today aern't ya :)
How can they tell from whalemeat samples today what size populations were a century ago?

Small populations become inbred and don't have much genetic variation. The amount of variation increases over time in larger populations. The lack of such variation in humans and (even more so) in cheetahs implies that in the relatively recent past both have gone through population bottlenecks - a fall to only a few thousand individuals.

Whales seem to have a great deal of variation for a population their size, implying that their population in the past was far far higher.
Offhand, I'd say probably fairly strong on the face of it. The article doesn't give figures for the number of samples taken, or the amount of difference between them, or the method used, and of course mistakes are always possible, but the general principle is well-understood and has been applied to various other species uncontroversially.

Assuming the variation rate they found is real, there could in principle be factors generating that without much larger populations, but they wouldn't normally generate diversity outside small parts of the genome, which would probably limit their overall impact.

In general, we'd probably be talking about situations where variation for its own sake is selected for - such as in the immune system, where often being different from your associates is an advantage as it reduces the chance that something that will infect them well will also infect you well. That sort of hybrid vigour ("heterozygote advantage") is also found in carriers for sickle-cell anaemia and thalassaemia, who are thought to be relatively resistant to malaria, and possibly carriers of cystic fibrosis, who (it has been suggested) might have been better able to drink milk - helping with calcium levels - during the last ice age when their skin didn't get much sunlight (which would often lead to rickets). This would explain CF being much more common in European and Europe-derived populations.

So yes, there are mechanisms which can drive variations rapidly through a popuulation. I wouldn't guess that there would be enough to skew the overall amount of variation in a whole genome, though.
A good question, and I can't remember the answer offhand. I'll try to get back to you on that one.
I have a copy of the paper. I'll let you know, assuming I understand any of it.
Okay - I've read the paper, and it's starting to come back to me.

Thinking of the amount of variation as a cone is a good start. However, it doesn't increase forever, because variants are lost from the population too. At some point, the number of variants arising will be balanced by the number being lost, and this equilibrium level depends on the mutation rate (which governs the rate of creation, of course) and the population size.

So for a steady population you have a roughly steady amount of variation, all other things being equal. If this population falls, the amount of variation will start to fall too, but the variation isn't all lost immediately. At the moment, when the population is low, we can make an minimum estimate of the previous population level. If the population stayed at its current level for many generations, the excess variation - and therefore the information about the previous population level - would be lost.

I don't know offhand how many "many" generations is for this purpose.
Coincidentally, I've just been watching an OU programme about statistical models of blue whale populations. It contained some horrible historical footage of whale hunting, and a quote attributed to a hunter, "If whales could scream, noone would hunt them, they couldn't bear the sound. The whales must be in agony."
Well, yes. There have been articles about how long whales take to die, and while it's usually only a couple of minutes, it can be a very long time. Over an hour in some cases.

Apparently Japan's threatening to leave the IWC this year if they aren't allowed to resume commercial whaling.
does this counter balance the fact that there was a newstory 2 maybe 3 months ago about the single whale song that keeps getting tracked which look like it's from the last of a species?

(whalers son)
I don't know, actually.

My guess given that we're not missing any large species previously known by whalers or from recent remains is that it'd probably be an individual with a weird song rather than a separate species, but I guess there's no way to know for sure.
Interesting. I'll try to get a copy of the paper from work. We may have a sub to that journal.

Odd. The consensus seems to be that it's a one-off of some sort, perhaps a deaf whale or a hybrid (surprising as that sounds). Its calls and travels don't seem to resemble any one of the baleen whale species more than the others, although they seem convinced that it is a baleen whale.

I think the fact that the calls weren't detected until about 1989 in spite of detector arrays having been around in the area since the fifties probably rules out it being the last of anything.