One comparison I came across compared the genome to a phone directory: the functioning part of the DNA is the phone numbers, the 'junk' DNA is the names and addresses, and the instructions on how to use the book. Still essential to the working of the genome, even if it doesn't actually code for any proteins.

Resin

This looks like a case of apples and oranges, two different ideas being conflated. On the one hand is genome size, which is a function of chromosome number and chromosome size. In this connection, genome size is generally uniform in a conifer genus. Spruces can be expected to have pretty similar-sized and structured genomes, but differ from each other in the mutations that have occurred. In angiosperms the situation is much more variable because of species that have arisen by chromosome doubling -- willows are an example.
The other idea is the proportion of junk DNA within the genome. Lots of junk is not equivalent to a larger genome; just the way the genome is divvied up.

I just read in The Washington Post a more extensive summary of the recent research findings on how DNA functions. There has apparently been a rather large number of studies of this general issue done by a number of researchers. The whole issue is so much more complicated than previously thought. They have found that genes overlap and some of the "base pairs" that operate in one gene also simultaneously operate as part of another or others. And, yes, resin, only a small percentage of the DNA it appears is actually involved in coding for proteins, but is involved in other kinds of functions that I can't begin to understand on the basis of the summaries I read.

I had wondered if all spruce trees might have similar sized genomes.

pinetree--yes, I had some familiarity with the doubling of chromosomes--if I remember right it is called polyploidy or something like that. Many, many years ago as a botany undergrad I was a field assistant to a professor who was studying the alpine flora of Mexico. One of the professor's collaborators joined us from time to time to take chromosome samples. One of the interesting aspects of this kind of flora was the isolation of populations on mountaintops. Another factor, if I remember right, that isolated populations was polyploidy. And sometimes these polyploids looked exactly like the species they had arisin from, but because of the doubling of chromosomes they were effectively isolated from each other.

Well, I didn't continue my botanical studies so all I learned during that time is just faded memories. But the whole issue still fascinates me. How a string of DNA of some 3 billion or so base pairs can create something as complex as a spruce tree or a human being always boggled my mind (yes, 3 billion is a large number, but it seems small to me if I consider all the complexity of the human body and its biochemistry). But now that the very complex interactions between genes and other elements of arrangement of these base pairs are coming to light, it may make more sense.

As a perhaps unrelated example of the potential complexity of our make up, I once read that the possible number of states of organization in the human brain is equal to the total number of all the elemental particles in the universe. By elemental particles I understand that to mean protons, neutrons, and electrons. Now that is a mind blowing number if you consider that the universe contains billions of galaxies each with billions of stars, etc.. At my university I had a friend who was a physics professor, so I blew this idea past him as something that seemd totally impossible. He boiled the number of elemental particles in the universe down to a number of 10 to the ? (I can't remember the number he gave) power, and then we did a little speculation about the neurons in the brain and the number of possible connections each one can have to a rather large number of others which in turn are connected to still others, etc. etc. In the end he thought the validity of this equivalence was not entirely out of the question.

Anyway, I bring this up just to illustrate the point that when individual elements (DNA base pairs) begin to interact with each other the complexity absolutely explodes, and then, forgive me, "anything is possible."

--Spruce

Still getting back to basics ... matching a tree to the environment it's genome evolved in will be the deciding factor in it's survival.

So although a Red Maple may be robust in your eyes planted here where I live it will barely survive. The genotype is what is playing the key role .. simply what genes are present not the mechanism of their regulation.

When you say "adaptability and variability" are you refering to developemental plasticity ?

On another note I have read recently that organisms can aquire traits via regulating protiens and pass those traits on to offspring. So a gene or genes turned off in a parent can be sent turned off to offspring.

La Marck is dancing in his grave.

Are NS strictly diploid? Reason I ask, there used to be an outfit here in Appleton called "Institue of Paper Chemistry". It was a big deal and included a forest genetics division, tree plantations etc. A guy who used to work there once mentioned a certain NS they were working with on the municiple golf course. It seems he said it was triploid or something. Could this be?

The tree is still standing-this conversation happened about eighteen yrs. ago-and if I remember right, has always had an extra rich coloration to its foliage as well as a certain robustness.

The trail's gotten cold, but maybe I could track the guy down and see if he remembers. Incidentally, another conifer they did much work with was larch. Many seed sources and hybrids were investigated. There are a handful of these around town now. Great trees.

+oM

Mohave:

Well, Nevada is a quite different kind of region from what we have in the eastern half or so of the country. What I have observed with red maple is that it grows as a bottomland species, but also, at least here in the mid Atlantic region of the country, it grows on dry ridgetops, and everywhere in between. And on all kinds of soils. It also has amazing variability in growth form, sometimes with very large leaves, sometimes very small. Sometimes it grows with a very regular form, and sometimes nearby it grows in almost grotesquely contorted and irregularly spreading forms, sometimes with pronounced spiral ridges on the trunk. And the bark! I have seen trees up to three feet in diameter with perfectly smooth silvery bark, and then I have seen trees with the very, very shaggy bark in loosely hanging plates more shaggy than shagbark hickory. And I have seen red maple bark that could fool the best forester into thinking it was sugar maple if seen from more than 5 feet away. And, of course the color variations in fall are really very, very wide. And in view of all the discussions we have had here about the compartmentalization of decay, as a logger/timberman I have seen some red maple trees that can compartmentalize decay to a remarkable degree, and others that seem to have no abilities of that kind at all. I am sure my casual observations don't begin to scratch the surface of the variability in this tree.

One more note about the variability in Norway spruce--I have given descriptions of this elsewhere--I like the more weeping forms, and one really noteworthy difference in these weeping forms is that some have the branchlets fall down away from the primary branches so the top of the branches are essentially bare and exposed. Others produce lots of new buds along the top of the primary branches and then again on top of the small secondary branches on top of them (compounding, so to speak) so that the tops of the primary branches become like carpets of green, sometimes as much as a foot wide with older trees. I think this is an especially attractive form, but I know of no cultivar that captures this. I think it would be worth making a selection for this characteristic.

--Spruce

Wisconsitom -- triploids arise from fusion of a normal gamete with an "unreduced gamete", i.e. which has escaped the reduction division of meiosis. So the nuclei all have three sets of chromosomes. Since if it crosses with a normal diploid, one set will have nothing to pair with, the triploid can only be reproduced vegetatively (by cloning). That limits the usefulness of triploids that seem to have promise. I knew that guy at the IPC but cannot recall his name. Getting soft in the head!

Yeah...I read that dogs have more than twice as many chromosomes as cats do, and if the canine genome is thus much larger (not necessarily true), does that partially explain the greater variability in the species?

Spruce, are there any other tree species that you have noted to display exceptional variability? The one I notice this most with is Bur Oak.

I heard a biology prof a few years ago say that Ailanthus altissima had very little variability. He felt this indicated an adaptive disadvantage, at least at the evolutionary time scale. That certainly struck me as counterintuitive, given that species' pehnomenal adaptability to many of today's ecosystems.

>Still getting back to basics ... matching a tree to the environment it's >genome evolved in will be the deciding factor in it's survival.

A species can have a large genome because the species recently (on an evolutionary time scale) underwent a genome duplication event. The resulting functional redundancy allows the accumulation of more genetic variation that could easily lead to greater adaptability, of both individuals and populations. Cartainly some tree species are more adaptable than others when it comes to soil type, moisture levels, sun exposure, etc.

>So although a Red Maple may be robust in your eyes planted here where I >live it will barely survive. The genotype is what is playing the key role .. >simply what genes are present not the mechanism of their regulation.

I have to disagree with that statement. Researchers recently sequenced the oppossum genome because that species is part of a group that diverged from the rest of the mammals so long. They were surprised to find how little the genes present differed from those of other mammals. They did find that expression levels of many genes were much different.

In addition, various transgenic experiments show over and over that changing expression levels of single genes can have large phenotypic consequences, oftentimes driving researchers crazy!

Alex

I just read another article summarizing recent research on genetics, this one in "The Economist," a news magazine that does not get the readership it deserves because of its name. It is not a magazine for economists, although it does cover the business world along with culture, politics, and science, etc.(Of course to some, all these are at bottom, economics!) I think it is the most interesting news magazine I know. Published in the UK, which also offers a different perspective sometimes.

Anyway, this article was more comprehensive than the others I read, and focused on some other aspects of the research, most of which I can't really understand very well. But reading it has in a general way deepened my sense of the complexity of the issues involved in this new research. Good newsstands usually carry this magazine--look for it.

cacau: Interesting about burr oak, a tree that has always interested me, but which is not common here, so I have not had a chance to really observe its variability.

As for variability in other species that I have observed--really none that compare to Norway spruce and red maple. But among the spruces, I have noticed some good variability in Oriental and Colorado (blue), but not much in Englemann, or white spruce. Some trees always look exactly the same to me--red pine is a good example, and others, like American elm have some good variability in form, although most always more or less vase shaped, but not much variability in bark, leaf color or form, or other characteristics. With red maple and Norway spruce the variability seems to extend to absolutely every part of the tree, although there are limits to the extent of this variability. For example, I never see a Norway spruce with the kind of blue color a blue spruce has, although at times I may see faint hints of it. But other aspects of Norway spruce foliage can be amazing. I have even seen a Norway spruce with the kind of foliage an Oriental spruce has--small shiny needles, etc., so I was completely fooled!

I do not live in fir country, but my impression is that the firs don't have as much variability as the spruces. Resin, could this be true? Could there be reasons for it?

Among pines. eastern white pine shows some good, but not outstanding variability. Scots pine in this country used for Christmas trees comes in a variety of strains that are varied in color and some other characteristics, but I don't know if in the wild these trees show much tree-to-tree variability.

Again, back to Norway spruce and red maple--the variability I see is contained in individual local populations; it is not just variability from strain to strain growing in different regions!

--Spruce

Hi Spruce,

Firs can be very variable, so much so that species limits are often much disputed, as in the Abies delavayi - densa - fabri - forrestii - spectabilis complex. This is perhaps in a different way to Norway Spruce, in that identifying an individual to species can be very difficult. Another case is Abies borisii-regis, I found trees growing wild in a small area (less than a hectare) in Bulgaria, that if planted in an arboretum, might have been assigned respectively to A. alba, A. borisii-regis, A. cephalonica and A. nordmanniana.

Scots Pine is more like you describe for Norway Spruce, within clear limits. It is always easily recognisable as Scots Pine (whichever part of the huge range they are from), yet different specimens can look very different, things like cones with flat scales, cones with prominent hooked scales, and so on - though the cones are always deflexed down the branch, and always with a similar surface texture. Even the three accepted varieties (vars. sylvestris, hamata, mongolica) are virtually impossible to pin down on morphology.

Resin

Mohave:

Interesting you should bring up Lamarck. The summary I just read in The Economist discusses the issue in a couple of paragraphs. I won't quote, but I will try to summarize in a sentence or two. The article in The Economist spends much of its space discussing the activity and importance of RNA and its different kinds/forms. And one point brought up is that RNA can be active in a cell's nucleus and that it can effect changes in the DNA, and this kind of activity can be stimulated by environmental factors. The article is very cautious on what this really shows, but it goes so far as to say that it admits "wiggle room for the re-admission of Lamarck's ideas."

A few months ago I read an article about the speed with which so many disease-causing bacteria develop resistance to antibiotics and other "germicidal" chemicals. The speculation was that based on any understanding of the normally occurring randon genetic mutations, this should not be possible. The suggestion seemed very Lamarckian to me.

--Spruce

Spruceman, I think you are seeing Lamarck where he didn't tread. He had no idea that there was in existence what we now call genetic material, DNA, which like other material can be modified by a sufficient shock like heat or caustic volcanic gases (by one speculation). These are not commonly parts of a critter's environment, and there's no evidence their effects are anything other than highly unusual.

Pinetree:

Well, yes, of course. But I mention it only because the issue was discussed directly in the summary in The Economist. I would question whether The Economist article would have introduced the topic on its own if it were not brought up by at least one of the series of research studies it is trying to summarize. I think the mention of Lamarck in this context is only a way of referring to the most general concept, that some aspects of the make up of an organism as it has been affected by the environment can be inherited. I think the accepted idea for, perhaps more than a century, has been "in no way, absolutely." At this point I think the recent research is questioning the "absolutely" aspect of this. Of course the means by which this may happen are completely different from what Lamarck could have supposed, and may be contrary to what he may have, or could have imagined. Certainly the principle of "natural selection" is in no way contradicted by any of this recent research, as far as I can understand it.

But I do think the recent research as summarized by the Economist is causing scientists to do some really basic re-thinking of a whole host of issues related to evolution and the functions of DNA and RNA and how the coding in genes is expressed. The sense I get from all three of these summaries I have read is that some things very revolutionary are being discovered that are turning much of what we understood on its head. I am a subscriber to Scientific American, which is a popular science journal that tries to help people like me understand things we are not trained to understand, so I have hopes that in the next issue, or soon, they will follow the lead of these other publications and try to explain some of this.

--Spruce

Spruce ...

There is a lot you are trying to untangle ..

Sorry I can't find the article .. I referenced .. it was a basic article in Discovery Magazine. I filed it so as not to lose it ... yep.

The jist was that protein molecules were interacting with the environment and regulating genes. No big deal .. the exciting part was that the genes regulated retained there state of regulation even when passed to the next generation.

Not a gene mutation as one might see with exposure to chemicals .. radiation ect..

That is different then anything I remember in my college days in the 90's. I have not had time to follow up on the original research .. hope to soon.

Though I think you should check out the topic of "developemental plasticity".

Alex and all ..

Indeed you are correct ... my post was sloppy ... interesting I picked up a cactus species a few weeks back .. along with the standard species was a "Monstrose" form ... one could never tell by shape the two plants were indeed the same species .. a mutation made them completely different.

I believe "monstrose" is a mutation in a developemental gene.

Good Day ..