Gene Sharing Is More Widespread than Thought, with Implications for Darwinism
David Coppedge.
Evidence is growing that organisms share existing genetic information horizontally, not just vertically. This has immense implications for neo-Darwinian theory that are not yet fully recognized. If traits can be shared across species, genera and even phyla, they are not being inherited from common ancestors. The findings might also cast stories about convergence and co-evolution in a completely different light. Let’s look at some of the news on this front.
Introgression
Last month, Current Biology posted a Primer on Introgression by four authors. Introgression refers to “lasting transfer of DNA from one of the species into the genome of the other” by means of hybridization and backcrossing. Basically, it describes “the incorporation of the DNA from one species into another.”
Over the last few decades, advances in genomics have transformed our understanding of the frequency of gene flow between species and with it our ideas about reproductive isolation in nature. These advances have uncovered a rich and often complicated history of genetic exchange between species — demonstrating that such genetic introgression is an important evolutionary process widespread across the tree of life
Figure 1 in this open-access paper shows nine photos of creatures where “gene flow” has been inferred. They include vastly different organisms, from bacteria to birds, fish, and mammals — including humans. The authors strive to maintain Darwinism in their explanation, but this realization undermines what previously was explained by convergence or by independent origins of traits:
Instead of waiting for a beneficial mutation to arise, gene flow can instead introduce variation that has been ‘pre-tested’ by selection, allowing species to evolve rapidly. For instance, alleles causing brown winter coat color in snowshoe hares (Figure 1E), early flowering time in sunflowers or serpentine soil tolerance in Arabidopsis have introgressed from closely related species, which has facilitated adaptation to new environments.
The authors do not speculate at this time how common adaptive introgression might be.
Kleptomania
In news from the Florida Museum of Natural History, biologists discussed how a new genome for ferns reveals “a history of DNA hoarding and kleptomania.” The article is classified under “Evolution” but what is Darwinian about it?
The “hoarding” part refers to ferns having 720 pairs of chromosomes “crammed into each of its nuclei” for unknown evolutionary reasons. Whole-gene duplication is not uncommon in plants and animals, but most species slim down their genomes over time. Why has this not happened in ferns? Geneticists are still trying “to figure out the evolutionary process underlying this paradox,” the article says.
The “kleptomania” claim refers to “the surprise discovery that ferns stole the genes for several of their anti-herbivory toxins from bacteria.”
Rather than evolving this toxin on its own, Ceratopteris appears to have obtained it directly from bacteriathrough a process called horizontal gene transfer. And given that there were multiple copies of the gene spread out among three separate chromosomes, it’s likely this happened more than once.
The article references a 2014 study that showed another instance of kleptomania. Ferns seem to have inherited genes for thriving in shade from distantly related plants, but “exactly how organisms separated by millions of years of evolution are able to swap fully functional genes remains unclear.”
“The mechanisms behind horizontal gene transfer remain one of the least investigated areas of land plant evolution,” Doug Soltis explained. “Over evolutionary timescales, it’s a bit like winning the lottery. Any time a plant is wounded, its interior is susceptible to invasion from microbes, but for their DNA to be incorporated into the genome seems amazing.”
These examples illustrate a sea change in thinking about horizontal gene transfer (HGT), which was formerly thought to be restricted to microbes.
Library Books
A related preprint by Haimlich et al. on bioRxiv investigated “Widespread horizontal gene transfer between plants and their microbiota.” Finding 180 genes that indicated “prevalent horizontal gene transfer,” they concluded,
Our results suggest that horizontal gene transfer between hosts and their microbiota is a significant and active evolutionary mechanism that contributed new traits to plants and their commensal microbiota.
Crediting evolution seems stretched, though. Information shared is not the same as information innovated, nor is borrowing a book as difficult as writing one.
Another preprint on bioRxiv reported introgression between “highly divergent sea squirt genomes” that were brought into contact by humans. The paper suggests that hybridization of these “incompletely isolated” species offered “an adaptive breakthrough” for the organisms. What other cases of assumed allopatric speciation convergence might turn out to be cases of introgression or HGT? Can life share library books of genes across distant species?
From Division of Labor to Expertise Sharing
Speaking of bacteria, Duke University proclaims that “Microbial Communities Stay Healthy by Swapping Knowledge.” How and why microbes do this prompted a metaphor that portrays intelligent action:
Put another way, a construction crew could be extremely resilient to electricians quitting if the plumbers on site also knew how to wire a building. But the same crew would be even more resilient if the remaining electricians could simply transfer their expertise to anyone on the job when needed, no matter their profession.
Dr. Lingchong You at Duke considers HGT a “dynamic division of labor” by which bacteria maintain their health in nature.
Human Sharing
With these reassessments of heredity in mind, how much of assumed “human evolution” could be explained by gene sharing instead of by the neo-Darwinian mutation-selection model? Have human beings been sharing library books or downloading each other’s software apps instead of writing them from scratch?
News from the University of Tübingen says that paleoanthropologists are considering the degree to which genetic hybridization affected the human skeleton and skull shape.
Many people living today have a small component of Neanderthal DNA in their genes, suggesting an important role for admixture with archaic human lineages in the evolution of our species. Paleogenetic evidence indicates that hybridization with Neanderthals and other ancient groups occurred multiple times, with our species‘ history resembling more a network or braided stream than a tree. Clearly the origin of humankind was more complex than previously thought.
It’s not the percentage of Neanderthal DNA that affects the phenotype, the researchers are finding, but “the presence of particular genetic variants” instead.
Similar conclusions are being reached at North Carolina State University where a news item says that “Ancient DNA caused a revolution in how we think about human evolution.” Out is the old single-file march of progress from ape to man. In is the “a series of streams that converge and diverge at multiple points.” The “exploratory study” going on at NC State is changing the view that evolution is driven by external environmental factors, such as climate, and toward the view that internal gene flow causes the variations in human anatomy.
Gene Flow Everywhere
The Tübingen story notes that evolutionary innovation by hybridization is being found everywhere:
In other organisms — from plants to large mammals — hybridization is known to produce evolutionary innovation, including outcomes that are both novel and diverse. “It is estimated that about 10 percent of animal species produce hybrids, including, for example, bovids, bears, cats and canids,” Ackermann says. Hybrids are also known in primates, our close relatives, such as baboons, she says. “Because hybridization introduces new variation, and creates new combinations of variation, this can facilitate particularly rapid evolution, especially when facing new or changing environmental conditions.”
A question arises whether these variations and combinations of variations are random when introduced by gene flow instead of mutation. If the latter, then old-school Darwinians might argue that they are merely additional manifestations of neo-Darwinism’s unguided process of random variation and selection.
But if these shared genes are instead modular pieces of functional information that are pre-adapted to join up in certain ways, then biologists will need to consider whether the source of that information requires an intelligent cause. The case for intelligent design in instances of gene flow can be further strengthened by observing whether newly incorporated genes are epigenetically regulated, targeted to functional loci, and responsive to signals from the environment. If so, organisms have been equipped with mechanisms to ensure robustness to changing conditions. That implies Foresight.
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