Saturday, April 11, 2009

Exceptional convergent evolution in a virus

This paper showed nicely that common selection can lead to extensive identity in DNA sequences. Thus, sequence comparison cannot always be used for inferring time of separation. This is exactly the point made by my MGD hypothesis. When we see a human and chimp identity of ~98%, we must first ask how much of that is due to common selection. The MGD says that there is a lot. The data are completely consistent with a pongid clade with human as the outgroup. Common selection for evolution of high intelligence could lead to more identity between human and chimp than between human and orangutan.

Genetics. 1997 Dec;147(4):1497-507. Links
Exceptional convergent evolution in a virus.

Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ.
Department of Zoology, Institute of Cellular and Molecular Biology, University of Texas, Austin 78712, USA.
Replicate lineages of the bacteriophage phiX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

Also on the same topic
Genetics, Vol. 181, 225-234, January 2009, Copyright © 2009

Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence
Jonathan P. Bollback*,1 and John P. Huelsenbeck

* Department of Biology, Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark and Department of Integrative Biology, University of California, Berkeley, California 94720

1 Corresponding author: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, King's Bldgs., W. Mains Rd., Edinburgh, EH9 3JT, United Kingdom.
Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions—if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives—which likely overlap more in the details of their adaptive solutions—will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence.


Stripe said...

This "convergence" of traits would be most easily explained by the environment, not by a process of random mutation and natural selection.

Why do they use "evolution" to explain the observations?

gnomon said...

Indeed, the differential survival of variants in response to a change in environment is a trivial phenomena and a trivial problem to figure out. That is why it was figured out by 5 people independently in a span of 40 years in a small country. Wells, Matthew, Blyth, Darwin, Wallace. It should not be properly called evolution if evolution means increase in complexity.

One of the founders of neodarwinism Simpson said:" If the two (micro and macro) proved to be basically different, the innumerable studies on micro-evolution would become relatively unimportant and would have minor value in the study of evolution as a whole."

In my opinion, micro and macro are exact opposite. And you are right that what is being studies daily by scientists, natural selection and differential survival, is not evolution proper.

Stripe said...

But such a distinction is very unpopular.


gnomon said...

It is very unpopular and lacks hard argument or evidence. The MGD hypothesis provides the argument and evidence: mutation is mostly good for micro but mostly bad for macro.

Eighty years after "The Origin of Species," evolutionary biologist Theodosius Dobzhansky acknowledged there was still no hard evidence connecting microevolution and macroevolution. Unfortunately, since only microevolution can be observed within a human lifetime, Mr. Dobzhansky wrote, "We are compelled at the present level of knowledge reluctantly to put a sign of equality between the mechanisms of macro- and microevolution, and proceeding on this assumption, to push our investigations as far ahead as this working hypothesis will permit."

Professor Soren Lovtrup said this in his book Refuting the myth of Darwinism:
Dobzhansky is making a mistake in logic here. Evo leads to changes in the genetic composition of populations, and it also leads to the origination of populations consisting of new kinds of individuals. However, the information residing in the genome does not explicitly specify the nature of the organism in question, rather, it is utilized in the epigenetic processes responsible for the ontogenetic creation of living organisms. And the latter concern individuals rather than populations, and therefore it follows that a theory accounting for the origin of new forms of life cannot be a theory dealing only with populations.