Monday, May 22, 2006

Massive duplication of genes may solve Darwin's 'abominable mystery', etc

Two different stories only six days apart, about the sudden origin of the Angiosperms (flowering plants), which was Darwin's "abominable mystery":

"The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery." (Darwin, C.R., Letter to J.D. Hooker, July 22nd 1879, in Darwin F. & Seward A.C., eds., "More Letters of Charles Darwin: A Record of His Work in a Series of Hitherto Unpublished Papers," John Murray: London, 1903, Vol. II, pp.20-21).]

[Graphic: The yellow water lily (Nuphar advena), Yi Hu, Penn State.]

Massive duplication of genes may solve Darwin's 'abominable mystery' about flowering plants, EurekAlert, 11-May-2006, Barbara K. Kennedy, Penn State ... [Also at ScienceDaily &] The yellow water lily (Nuphar advena) shows evidence of an ancient genome duplication that may have been a key event in the evolution of flowering plants. Researchers from the Floral Genome Project at Penn State University, with an international team of collaborators, have proposed an answer to Charles Darwin's "abominable mystery": the inexplicably rapid evolution of flowering plants immediately after their first appearance some 140 million years ago. [If the origin of the angiosperms (a plant division - Anthophyta - equivalent to an animal phylum):

"Classification of Plants Plant biologists use the term division for the major plant groups within the plant kingdom. This taxonomic category corresponds to phylum, the highest unit of classification within the animal kingdom. Divisions, like phyla, are further subdivided into classes, orders, families, and genera ... Angiosperms: Division Anthophyta: Flowering plants" (Campbell, N.A., Reece, J.B. & Mitchell, L.G., "Biology," [1987], Benjamin/Cummings: Menlo Park CA, Fifth Edition, 1999, pp.549-550. Emphasis original)

one of the "four major periods of plant evolution":

"The fossil record chronicles four major periods of plant evolution, which are also evident in the diversity of modern plants ... Each period was an adaptive radiation that followed the evolution of structures that opened new opportunities on the land ... The fourth major episode in the evolutionary history of plants was the emergence of flowering plants during the early Cretaceous period in the Mesozoic era, about 130 million years ago. The flower is a complex reproductive structure that bears seeds within protective chambers called ovaries. This contrasts with the bearing of naked seeds by gymnosperms. The great majority of modern-day plants are flowering plants, or angiosperms (Gr. angion, `container,' referring to the ovary, and sperma, `seed')." (Campbell, et al., 1999, p.548. Emphasis original)

arose as the result of a "Massive duplication of genes," then it would not "solve Darwin's 'abominable mystery' about flowering plants" - it would confirm it! And indeed, falsify Darwin's theory (as a general theory), since: 1) this was a major new chapter in life's history; 2) which did not arise "by accumulating slight, successive, favourable variations" but by a "great or sudden modification":

"As natural selection acts solely by accumulating slight, successive, favourable variations, it can produce no great or sudden modifications; it can act only by short and slow steps. Hence the canon of `Natura non facit saltum,' [nature does not make leaps] which every fresh addition to our knowledge tends to confirm, is on this theory intelligible." (Darwin, C.R., "The Origin of Species By Means of Natural Selection," 1872, Sixth Edition, Senate: London, 1994, pp.413-414. Parenthesis mine)]

By developing new statistical methods to analyze incomplete DNA sequences from thirteen strategically selected plant species, the researchers uncovered a previously hidden "paleopolyploidy" [i.e. ancient polyploidy] event, an ancient whole-genome duplication that preceded the appearance of the ancestral flowering plant. The results will appear in the June issue of Genome Research. Claude dePamphilis, associate professor of biology at Penn State, is the principal investigator of the Floral Genome Project and the senior author of the paper. "We found a concentration of duplicated genes that suggests a whole-genome duplication event in the earliest flowering plants," he says. "A polyploidy event early in the history of flowering plants could explain their sudden evolution." ... [This may not be completely new. I remember doing a genetics assignment on polyploidy (i.e. the duplication of an entire genome) in 2002, and in at least one of the journal articles I drew upon said that the reason there is so much polyploidy in angiosperm species (~70%) is probably because of ancestral polyploid events.

But while polyploidy has been an important factor in generating new species of plants (it is comparatively rare in animals for several reasons), despite an entire genome being duplicated, the resulting new species is still within the same genus. Harvard botanist and Neo-Darwinism co-founder G. Ledyard Stebbins pointed out that "polyploidy has contributed little to progressive evolution":

"Polyploidy is a very common method of evolution in higher plants. Between one-fourth and one-third of the species of flowering plants are polyploid with reference to their nearest relatives. Familiar examples among crop plants are wheat, oats, potato, tobacco, cotton, alfalfa, and most species of pasture grasses. Familiar weeds and wild flowers which are polyploid are the eastern blue flag (Iris versicolor), meadow rue (Thalictrum spp.), some species of wild rose, chickweed (Stellaria media), miner's lettuce (Montia perfoliata), yarrow (Achillea spp.), and various species of violets and asters. Furthermore, there is evidence that polyploidy in the remote past has given rise to many genera and groups of genera such as the apples, olives, willows, poplars, and many genera of ferns. Nevertheless, polyploidy has contributed little to progressive evolution. In genera which contain both diploids and polyploids, the major trends of evolution are all represented by diploid species, and the polyploids serve merely to multiply the variations on certain particular adaptive `themes.' This is probably because the large amount of gene duplication dilutes the effects of new mutations and gene combinations to such an extent that polyploids have great difficulty evolving truly new adaptive gene complexes." (Stebbins, G.L., "Processes of Organic Evolution," Prentice-Hall: Englewood Cliffs NJ, 1966, Second printing, p.129)]

The reason is that two genomes (like two copies of the same edition of a book or newspaper) don't have any new information. It would take a very special (to put it mildly) duplication event to produce a new phylum!

South Pacific plant may be missing link in evolution of flowering plants: Novel reproductive process may point to ancestors of angiosperms, says University of Colorado study, EurekAlert!, 17-May-2006, Ned Friedman ...

[Graphic: Amborella leaves, University of Colorado, Boulder.]

A new University of Colorado at Boulder study involving a "living fossil plant" that has survived on Earth for 130 million years suggests its novel reproductive structure may be a "missing link" between flowering plants and their ancestors. The Amborella plant, found in the rain forests of New Caledonia in the South Pacific [It is significant that this plant occurs only in New Caledonia, because that island "is a fragment of the ancient continent of Gondwana."] has a unique way of forming eggs that may represent a critical link between the remarkably diverse flowering plants, known as angiosperms, and their yet to be identified extinct ancestors, said CU-Boulder Professor William "Ned" Friedman. Angiosperms are thought to have diverged from gymnosperms -- the dominant land plants when dinosaurs reigned in the Cretaceous and Jurassic periods -- roughly 130 million years ago and have become the dominant plants on Earth today. "One of the biggest challenges for evolutionary biologists is understanding how these flowering plants arose on Earth," said Friedman, a professor in CU-Boulder's ecology and evolutionary biology department, whose study appears in the May 18 issue of Nature. "The study shows that the structure that houses the egg in Amborella is different from every other flowering plant known, and may be the potential missing link between flowering plants and their progenitors."... [No doubt this is a `vestigial organ' (Amborella is itself an angiosperm) and therefore further evidence that angiosperms arose from gymnosperms (non-flowering seed plants like conifers), which I accept. But as Friedman correctly observed, below, that that does not change the fact that "The mystery remains abominable":

Ancient shrub unlocks a clue to Darwin's 'abominable mystery'. Christian Science Monitor, May 18, 2006, Peter N. Spotts ... To millions of moms, the Mother's Day bouquet still gracing the dining room table symbolizes gratitude and love. To Charles Darwin, however, they also would stand as colorful characters in what he called an "abominable mystery" - the origin of flowering plants. "It's no different now," sighs biologist William Friedman. The mystery remains abominable. .... [The reason is that, as would be expected in a new phylum, angiosperms have many "unique characteristics" that gynosperms lack, including "flowers, closed carpels, double fertilization ... and ... sieve tubes and companion cells in the phloem":

"The unique characteristics of the angiosperms include flowers, closed carpels, double fertilization leading to endosperm formation, a three-nucleate microgametophyte and an eight-nucleate megagametophyte, stamens with two pairs of pollen sacs, and the presence of sieve tubes and companion cells in the phloem ... . These similarities clearly indicate that the members of this phylum were derived from a single common ancestor. This common ancestor of the angiosperms ultimately would have been derived from a seed plant that lacked flowers, closed carpels, and fruits. The earliest known, clearly identifiable fossils of angiosperms are flowers and pollen grains up to 130 million years old, from the Early Cretaceous period ... . There are intriguing suggestions that much older fossils-up to 200 million years old-may have had some, but perhaps not all, of the characteristic features of angiosperms. Currently the interpretation of these fossils is enigmatic, and it appears most likely that the phylum did in fact originate in the Early Cretaceous (or perhaps uppermost Jurassic) period." (Raven, P.H., Evert, R.F. & Eichhorn, S.E., "Biology of Plants," [1971], W.H. Freeman and Co/Worth Publishers: New York NY, Sixth Edition, 1999, p.519)

For all these to arise from one "Massive duplication of genes" would be indistinguishable from a miracle (which I expect it was)!]

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'


Edward T. Babinski said...

STEPHEN JONES: Harvard botanist and Neo-Darwinism co-founder G. Ledyard Stebbins pointed out that "polyploidy has contributed little to progressive evolution"

ED: Stebbins wrote that way back in 1971. Since then geneticists have learned much more about duplications of individual chromosomes, and also about duplications of ENTIRE GENOMES. And no, the animals in such cases do not die from such a massive mutation. In fact two similar species of zebrafish live today, one with nearly twice the genetic material of the other, though many of the duplicated genes are pseuodgenes in the species whose ancestors underwent the duplication.

For instance, CONTRA STEBBINS,
in 1998 a "Computational Genetics Discussion Group: Genome Duplication" wrote on the web:

"Whole genome duplication appears to be an important evolutionary mechanism (Ohno, 1970).

"Despite the rarity of whole-genome duplications, we have observational evidence for several of them:

"Saccharomyces cerevisiae (yeast) duplicated about 10^8 years ago.

"Vertebrates underwent 2 duplications some 2*10^8 years ago.

"More recent genome duplications have occurred in some vertebrate lines such as frogs, the salmoniform fish and zebrafish.

"Particularly prevalent in plants (i.e. several occurences in the cereal lineage)."


"In 1999 Holland [a professor] lists understanding ‘the importance of gene duplication in the evolution of development’ as one of the two most important questions in evolutionary developmental biology at the end of the 20th century.

"This statement reflects the particular interest in duplications in developmental genes, but also the general interest in evolution by gene duplications."


Since then, "unmistakable" evidence for "whole genome duplication" in the vertebrate line of evolutionary changes has been found:

Two rounds of whole genome duplication in the ancestral vertebrate.

PLoS Biol. 2005 Oct;3(10):e314. Epub 2005 Sep 6. Related Articles, Links

<...> UNMISTAKABLE EVIDENCE OF TWO DISTINCT GENOME DUPLICATION EVENTS EARLY IN VERTEBRATE EVOLUTION indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.

Definition of *PARALOGOUS GENES*: "Two genes or clusters of genes at different chromosomal locations in the same organism that have structural similarities indicating that they derived from a common ancestral gene and have since diverged from the parent copy by mutation and selection or drift."


Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Nature. 2004 Oct 21;431(7011):916-7.

<...> ANALYSIS OF THE TETRADON AND HUMAN GENOMES SHOWS THAT WHOLE-GENOME DUPLICATION OCCURRED IN THE TELEOST FISH LINEAGE, SUBSEQUENT TO ITS DIVERGENCE FROM MAMMALS. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome" <...>

Edward T. Babinski said...
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Edward T. Babinski said...

Excerpts from: GENE DUPLICATIONS AND VERTEBRATE PHYLOGENY by James Cotton (circa 2001)

"Theoretical studies have shown that gene duplications may be relatively likely to lead to new gene functions, and to increase the fitness of genomes in which they occur. Walsh (1995) presents a population genetic model suggesting that, for large populations, ‘new gene function, rather than pseudogene formation, is the expected fate of most duplicated genes’, which would make gene duplication an impressively powerful mechanism for the evolution of novel biochemistry and novel developmental processes. Specifically, new functions are likely to evolve where rS >> 1, where S = 4Nes and Ne is the effective population size, S is the selection coefficient and r is the ratio of advantageous to other mutations. This model is likely to underestimate the rate of evolution of new gene functions, principally because it assumes that all nonadvantageous mutations are neutral, where in reality many will be more or less deleterious. Ohta (1989) admits that ‘gene duplication could well have been the primary mechanism for the evolution of complexity in higher organisms’, and presents models for the origin of ‘gene families with diverse functions’, concluding that natural selection should favour those genomes with more favourable mutations occurring in duplicated genes, so there should be selective pressure favouring mechanisms of gene duplication. Ohta has also presented a number of other simulation studies on the evolution of large gene families (Batson and Ohta, 1992; Ohta 1987, 1988a, 1988b), which broadly support the likelihood of this model in molecular evolution. Empirical studies (such as Nadeau and Sankoff, 1997) largely suggest that the evolution of new functions is even more common than theoretical studies suggest, but there are a number of difficulties with the empirical work (Wagner, 1998).

"The very existence of families of paralogous genes also provides powerful evidence for the importance of gene duplications, so data like those shown in figure 2 seem to confirm that gene duplications have indeed played a very powerful role in shaping genomes. Although, as discussed later, much interest has focused on gene duplications in vertebrates, there is substantial evidence (e.g. Brenner et al., 1995; Wolfe and Shields, 1997) that gene duplications have also been important in other organisms, such as in the evolution of cell-to-cell communication pathways in the first multicellular animals (Suga et al., 1999. Ono et al, 1999). It is also important to note here that a number of potential mechanisms for gene duplication have been suggested, ranging from unequal crossing-over, which will lead to duplication of a relatively small stretch of DNA, to polyploidisation, which will lead to duplication of the entire genome."

Stephen E. Jones said...


>Edward T. Babinski said...
STEPHEN JONES: Harvard botanist and Neo-Darwinism co-founder G. Ledyard Stebbins pointed out that "polyploidy has contributed little to progressive evolution"

>ED: Stebbins wrote that way back in 1971. Since then geneticists have learned much more about duplications of individual chromosomes, and also about duplications of ENTIRE GENOMES. And no, the animals in such cases do not die from such a massive mutation.

As I said, it is *rare* (not non-existent) in animals and common in plants.

>In fact two similar species of zebrafish live today, one with nearly twice the genetic material of the other, though many of the duplicated genes are pseuodgenes in the species whose ancestors underwent the duplication.

Thanks for making my point: they are still "two *similar species* of zebrafish"!


>"Whole genome duplication appears to be an important evolutionary mechanism (Ohno, 1970).

That all depends on what the all-flexible word "evolution[ary]" means.

Ohno (whose book I have a standing order in for, but it is *very* rare) certainly did not regard it as *Darwinian*:

"As pointed out by Haldane ([Haldane J.B.S, "Natural Selection," in Bell P.R., ed., "Darwin's Biological Work," Cambridge University Press: Cambridge UK, 1959, p.117-124]), elimination of deviants to keep the status quo (in the form of "centripetal selection") is the most common type of natural selection. Also a remarkably conservative nature of natural selection has been brought to light by Ohno (Ohno, 1970) in his discussion on the role of gene duplication in evolution. What has been revealed by recent studies of molecular evolution is again the prevalence of this type of natural selection." (Kimura M., "Population Genetics and Molecular Evolution," The Johns Hopkins Medical Journal, Vol. 138, No. 6, June 1976, p.260)

"This is what an American geneticist has to say on the subject: `Yet, being an effective policeman, natural selection is extremely conservative by nature. Had evolution been entirely dependent upon natural selection, from a bacterium only numerous forms of bacteria would have emerged. The creation of metazoans, vertebrates and finally mammals from unicellular organisms would have been quite impossible for such big leaps in evolution required the creation of new gene loci with previously nonexistent functions' (Ohno, 1970). All this is rather obvious, but if people wilfully close their eyes to it, they will not see." (Grasse P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," [1973], Academic Press: New York NY, 1977, pp.217-218)

"It is possible that tandem duplication of one or several genes could produce a marked increase in the amount of genetic material over only a few thousand generations, but it is doubtful that any marked functional diversity could arise in this way. Indeed, quite the reverse. In writing about the lungfish. S. Ohno remarks: `By establishing such a system [tandem duplication] the organism effectively forfeited an opportunity for further evolution. In a manner of speaking, the genome became frozen, while containing enormous genetic redundancy. It is clear that in doing so such a lineage reached an evolutional dead end. It will be shown that what happened to the lungfish also happened to salamanders and newts.... Indeed, this side branch stopped dead at the amphibian stage.'" [Ohno S., "Evolution by Gene Duplication," Springer-Verlag: New York, 1970] (Hoyle F. & Wickramasinghe C., "Evolution from Space", [1981], Paladin: London, 1983, reprint, p.105).

"At all events, tandem duplication does not solve the evolutionary dilemma. It might give a rapid increase in the quantity of genetic material, but it only does so by being highly repetitive, and this will not give a sequence of 'quantum jumps' in the forms of plants and animals, such as is needed to provide for the divergent evolutionary branches shown in Figures 6.6 to 6.10. Repetitions will give some changes, of course, by altering the quantities of certain proteins, but, as Ohno remarks in the above quotation, the changes are much more likely to be stultifying than to lead to adventurous new possibilities." (Hoyle & Wickramasinghe, 1983, p.106).

"To speed the fixing of neutral mutations, Dr Ohno requires the ancestral breeding group to have been rather small. The free genes then go in biochemical directions that have little to do with natural selection. In this way a gene can drift, even within a reptile, to a form that will be of later use to man. Indeed, the genes are supposed to have drifted to a configuration which determined the later evolution of Figure 6.10, and the still later evolution of Figure 7.2, not by the need to adapt to the immediate environment, but by chance. The chance anticipation of later need continued even up the last stage of Figure 7.2. Thus in his concluding pages Dr Ohno remarks: `Did the genome of our cave dwelling predecessor contain a set or sets of genes which enable modern man to compose music of infinite complexity and write novels with profound meaning? One is compelled to give an affirmative answer .... It looks as though the early Homo was already provided with the intellectual potential which was in great excess of what was needed to cope with the environment of his time.' [Ohno S., "Evolution by Gene Duplication," Springer-Verlag: New York, 1970] Dr Ohno was thus led by his resolute respect for the biological facts to what seems to us a non-Darwinian position almost as marked as our own. The facts, interpreted within a terrestrial theory of the origin and evolution of life, force one to suppose not only that chance faced up to the incredibly minute probability of discovering the enzymes and other basic biochemical substances, a probability we calculated in chapter 2 to be less than 10^40, 000, but that chance mutations also produced genes which were to prove capable of writing the symphonies of Beethoven and the plays of Shakespeare. This is the position to which one is inevitably led by following an Earth-bound theory, a position that we believe to constitute a reductio ad absurdum disproof of that theory." (Hoyle & Wickramasinghe, 1983, pp.106-108).

As I said, IIRC, mere duplication of an entire genome adds no extra information.

And as I said, IIRC, it must have been a *very special* genome duplication that created an entire *phylum*, the angiosperms. Such an event would be indistinguishable from a miracle (which I assume it *was*)!

Stephen E. Jones