26 December 2007

Beacon Valley looking northeast toward Taylor Glacier

Do thawing glaciers speed up evolution? This possibility is endorsed in a study of DNA buried for eight million years in the Mullins and Beacon Valleys of Antarctica. The research team from New Jersey and Boston noticed that the frozen DNA slowly degrades, perhaps because ionizing radiation from space is poorly shielded in Antarctica. Nevertheless, whole bacteria have remained viable there, and even killed microbes retain functional DNA that may be redeployed in the biosphere. Unexpectedly, among 559 frozen genes sequenced, the team found that 248, or 44%, have no known terrestrial orthologs. The researchers write:

"The community DNA immobilized in Antarctic ice is essentially a 'gene popsicle,' which can potentially be acquired by extant organisms upon thawing.... Given the widespread influence of lateral gene transfer (LGT) within microbial populations and its putative influence on the tempo of microbial evolution..., one can envision periods in Earth's history when large numbers of ancient genes became available as ice sheets melted. Indeed, the tempo of evolution after major global glaciations appears to have increased dramatically..., although causal mechanisms have been poorly defined."

19 December 2007
The ancestor of earthly life was molecularly complex. This is the essential conclusion of a study of protein architecture by a team from the University of Illinois at Urbana-Champaign. The researchers believe that protein fold and fold superfamilies are better conserved than sequences of nucleotides or amino acid residues, and that this conservation makes them better for analysing the deepest past. They observe —

• We ...found that architectures at the base were omnipresent or common to all superkingdoms....
• Older architectures are more abundant and diverse.
• ...The repertoire of architectures in proteomes can be regarded as a collection of historical imprints or molecular fossils preserved in nature by successful propagation and evolutionary 'lock-in'....
• Our analysis ...suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya.
• The diversity of ancient architectures common to superkingdoms suggested that the universal ancestor had a complex and relatively modern eukaryotic-like organization and hinted at a prokaryotic world stemming fundamentally from reductive evolutionary processes.

12 December 2007
Shuttle experiment to study effects of space on bacterial spores. Wayne Nicholson, an astrobiologist at the University of Florida, plans to submit Bacillus subtilis to the rigors of space on the EXPOSE platform, scheduled for delivery to the International Space Station on the next shuttle flight. After more than a year, the samples will be returned to Earth and tested for survival, and for genetic and physiologic changes induced by space exposure. The experiment should help NASA to anticipate any possible contamination of life-detection equipment aboard future Mars landers. "Life has all sorts of tricks up its sleeve," Nicholson said. "I can't wait to find out what it comes up with."

10 December 2007
When eukaryotes are included in our considerations of evolution, the phylogeny of life seems better represented by a network than a tree.... — James O. McInerney and Davide Pisani, biologists at the National University of Ireland, commenting on an extensive study of horizontal gene transfer based on microbial genome sequencing that makes use of E. coli. They also note:

• ...Among 246,045 genes from 79 different species of prokaryotes, there was no single gene that, along with all its prokaryotic homologs, resisted... gene transfer by transduction....
• The stealth model of successful horizontal gene transfer implies that it may be easier to introduce DNA from a distant relative ...than from a closer relative.
• ...The existence of a prokaryotic Tree of Life remains an open question.

29 November 2007
Surprises come from a comparison of twelve fruitfly genomes, the focus of a special section in Nature. The primary study was motivated by the premise that complete sequences of many closely related species should lead to new insights about evolution. The genomes of two of the fruitfly species had been sequenced earlier; ten more were recently completed.

For one surprise, "A new gene called drosomycin, which codes for an antifungal compound, appears only in D. melanogaster and its close relatives. There are no clues, however, as to how this gene came to be," comments Elizabeth Pennisi. In fact, the Consortium observed, "All species were found to have novel genes not seen in other species. ...Similarly,... total genomic transposable element content varies substantially among species, and several instances of lineage-specific transposable elements were discovered."

"...The apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this evolutionary revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species. This is the reason the 12 species only share 77 percent of their genes," says Consortium member Matthew Hahn.

On the other hand, the Consortium notes, "The vast majority of multigene families are found in all 12 genomes...." Furthermore, "Most functional categories of genes are strongly constrained."

Cosmic Ancestry predicts that darwinian evolution, by itself, can change genetic programs only within narrow ranges, and that new genetic programs must be imported by various mechanisms of gene transfer. If so, comparisons among related species should find functional genetic sequences that are either very similar (confined within narrow ranges), or not-at-all similar (imported). We think the Drosophila study supports that view. And we were impressed to learn that, even among fruitflies, there would be so many genes unique to each species. This indicates that gene transfer supplies, in addition to programs for major new features, programs and subroutines for a wide variety of metabolic and other processes.

19 November 2007
Ancient retroviruses spurred evolution of gene regulatory networks in humans and other primates. That's how The University of California summarizes new research led by a team at its Santa Cruz campus. There, Tim Wang at al. studied a gene designated p53, which functions as a "master gene regulator" among primates but not among other mammalian species. They wanted to know how p53 acquired its powerful function.

By analyzing and comparing genetic data from different species, the team estimated that certain endogenous retroviruses (ERVs) entered the genome about 40 million years ago, and spread rapidly in primates about 25 million years ago. Apparently, these retroviruses supplied the coding that gave p53 its master regulator capability among primates.

Following this work, the team has proposed a new mechanism for evolutionary change. "Conventional wisdom says that evolution is driven by small changes — point mutations — to the genetic code. If a change is beneficial, the mutation is passed onto future generations."

"Now it appears that another level of evolution occurs that is not driven by point mutations. Instead, retroviruses insert DNA sequences and rearrange the genome, which leads to changes in gene regulation and expression. If such a change in gene regulation is beneficial, it is passed onto future generations."

Interestingly, today an estimated 8 percent of the human genome consists of recognizable endogenous retroviruses.

"ERV-mediated expansion of a gene regulatory network probably happened more than once and not just in primates. We predict it led to other master gene regulators, not just p53."

25 October 2007
You can think of the genome as a revolving door—genes keep coming and going — Matthew W. Hahn

Geneticists at Indiana University, comparing the completed genomes of six species (rhesus macaque, dog, rat, mouse, chimpanzee and human), report that the rate of gene turnover in humans is more than 2.5 times faster than in other mammals. They conclude,

• A disproportionate amount of gene gain and loss has occurred between humans and chimpanzees.
• There has been an acceleration in the rate of gene gain and loss along the primate lineage, especially among the great apes.
• Several gene families... have undergone copy number changes large enough to suggest the influence of natural selection.
• Summing across all families, we infer the gain of at least 678 genes in the human genome and the loss of 740 genes in the chimpanzee genome since their split 5-6 million years ago; these results imply that 6.4%... of all human genes do not have a one-to-one ortholog in chimpanzee.
• This genomic revolving door... must certainly account for human adaptations due to both recent gene duplications... and recent gene losses.
• The accelerated rate of evolution in primates further suggests that duplication and loss of genes has played at least as great a role in the evolution of modern humans as the modification of existing genes.

We welcome these insights. And we have a question. Hahn et al. assume that if a gene is present in one lineage and absent in another, the latter must have lost it. But alternatively, the former might have gained it from beyond the lineages under study, by a variety of gene transfer mechanisms. Yet in their new report, the word "transfer" does not appear. Why?

20 October 2007
New genetic functions arise when selection is imposed on a minor side function of a preexisting gene. This is the thesis sentence of a solution to "Ohno's dilemma" now proposed in PNAS by a Swedish and two American biologists. They explain,

• New genes with novel functions arise by duplication and divergence, but the process poses a problem. After duplication, an extra gene copy must rise to sufficiently high frequency in the population and remain free of common inactivating lesions long enough to acquire the rare mutations that provide a new selectable function. Maintaining a duplicated gene by selection for the original function would restrict the freedom to diverge. (We refer to this problem as Ohno's dilemma).

• The parent gene encodes a protein, which (like many proteins) provides not only its primary selected function, but also a variety of minor activities that are neither beneficial nor deleterious before the process starts (...activities "b," "c," and "d").
• The process of forming a new gene is initiated when a change in the ecological niche... makes one of these minor activities valuable and imposes a selection for an increase in its level.
• Alternatively selection could be imposed first and a new mutation could confer a trace of the beneficial side activity before duplication of the parent gene.
• In either case, the parent allele possesses a trace of the new valuable activity. Selection will then favor any increase in the level of this trace activity....
• The same selection that favored amplification can favor improvement in the amount of the new activity provided by any single gene copy, all of which are targets for improvement....
• Mutations that improve different gene copies can be assorted by recombination between copies to make new combinations that improve the functionality of some individual copy....
• [Minor secondary activities] go unnoticed when the gene is in single copy....
• In populations of multicellular organisms [eukaryotes], weaker selection may be sufficient.... Furthermore, in these organisms even tandem repeats seem less unstable than in bacteria. Finally, in smaller populations initial duplications will be less subject to selective loss.... Thus the process of new gene evolution is likely to require positive selection for the new activity as outlined in the model presented here.

Two years ago we reviewed an article explaining subfunctionalization. In that process a single gene with two functions undergoes duplication, yielding two genes, each with one of the original functions. Following the separation each gene may be further optimized by natural selection operating on point mutations. And stress may enhance the mutation rate, as today's researchers note.

In fact, the current study seems to be entirely about subfunctionalization, now seen as ubiquitous. Bergthorsson et al. emphasize that many genes have second (or third or fourth...) functions that may be weak or inactive initially. When called to active duty, these can supply functions not previously expressed. By our reading, the current study suggests that subfunctionalization is the source of most new functions in all forms of life. Wow.

Could the remainder be supplied by gene transfer? If so, evolutionary innovation occurs when genetic programs already in existence — among present genes or ones installed by transfer — become deployed and optimized. All of these steps are supported with plausible models and good evidence. Where genetic programs come from "in the first place" is not answered, or even asked, here. But if they can arise de novo in the darwinian manner, why is the supporting case so weak and unconvincing?

8 October 2007
Cosmology may look like a science, but it isn't a science — James Gunn, Professor of Astronomy, Princeton University

New analysis suggests that the universe may have a preferred axis or even be rotating. Another surprise for cosmology? In the all-sky image from NASA, connected black dots noted ?–? designate the the suggested preferred axis, the galactic axis is vertical, and black squares specify the solar system axis.