Epigenetics - The reasons why organisms can quickly adapt to changing environment

Random mutations and selection are not the reasons why organisms adapt to changing conditions

https://www.forbes.com/sites/grrlscientist/2017/09/06/how-do-darwins-finches-respond-so-quickly-to-environmental-changes/#37f1f45a5810

Excerpt: "How does a population adapt to sudden changes in the environment? According to the most widely accepted paradigm, random genetic changes (mutations) are the source of heritable changes in a plant or animal’s observable characteristics (phenotype). Phenotype, in turn, is the raw material that is acted upon by natural selection, and the most beneficial adaptations are passed on to successive generations. But there is a problem with this paradigm: adaptive genetic mutations are so infrequent that this scenario cannot adequately explain the speed at which adaptation can occur.

One well-known example of speedy adaptation is seen in “Darwin’s finches”; a group of approximately 15 bird species that live in the Galápagos Islands Archipelago, which are located on the equator in the Pacific Ocean. Ongoing field studies have documented rapid changes in these birds’ beak sizes and shapes in response to sudden environmental variations -- drought, or human disturbances, for example -- yet very few genetic changes have been found that accompany those physical differences between finch species, nor between populations. What guides these important changes and the speed which they can occur in these iconic birds?

The process of adaptation is more subtle than originally thought

Scientists have recently become aware that adaptation is not solely dependent upon genetic mutations; it can also occur through “extra-genetic” mechanisms. At least some changes in gene function and expression patterns are independent of mutations in a gene’s DNA sequence, yet these changes may still be inherited. These alterations are known as “epigenetic changes” (epi comes from the Greek, and translates as “over, outside of, around”) because these changes are in addition to changes in the DNA sequence itself. Epigenetic changes can activate or intensify, lessen or even completely silence, the activity of a particular gene without changing its DNA sequence.

Epigenetic changes can be triggered by environmental events. The changes that dominate alterations in gene expression and function are biochemical in nature, including: addition of a biochemical tag (methylation) to DNA; addition of a biochemical tag (methylation or acetylation) to the histone proteins around which DNA spools; or regulation of gene expression patterns by small RNA molecules.

Probably the most common epigenetic modification is DNA methylation, and just as genetic mutations can be heritable, DNA methylation patterns can be heritable, too. For example, previous work found that some epigenetic variations in five closely related species of Darwin’s finches accompany genes associated with beak size and shape, as well as a number of other important physical traits. We also know that changes in DNA methylation patterns are more common than DNA mutations. Based on these clues, a team of researchers, led by evolutionary ecologist Sabrina McNew, a graduate student at the University of Utah, proposed that epigenetic mutations -- NOT genetic mutations -- may explain how Darwin’s finches rapidly adapt to new or highly variable environments, such as those created by urbanization.
 

“Darwin’s finches are known for being phenotypically very variable, yet [they are] genetically pretty similar,” Ms. McNew explained in email.

“We were interested in investigating epigenetic variation between urban and rural populations [of Darwin’s finches] because other exciting recent work suggests that epigenetic mechanisms, such as DNA methylation can be a source of heritable phenotypic variation.”

Are epigenetics the secret to Darwin’s finches’ speedy adaptation?

To test this hypothesis, Ms. McNew assembled a research team and they measured physical traits (morphology) of wild birds in the field, and examined both the genetics and the epigenetics of separate populations of two Darwin’s finch species living at El Garrapatero, a relatively rural, undisturbed locality. They compared these findings to those from urban finch populations living near Puerto Ayora (Academy Bay), the largest town in the Galápagos Islands.

The rural and urban study sites are separated by about 10km. Earlier long-term studies (2002–2012) established that the birds in these two finch populations stay put: only one bird (a female medium ground finch) out of 300 marked and recaptured individuals relocated between the two study sites in one decade.

“[T]he finches tend to be fairly sedentary and so we think that most of the birds we caught probably grew up at whichever site they were caught at and probably their parents lived there too,” Ms. McNew said in email.

Both sites are located on the southern and southeastern coast of Santa Cruz Island, and feature the same scrubby arid habitat. Despite the habitat similarities between the rural and urban sites, there is one big difference: urban-dwelling finches dine on a banquet of human foods that are new to them whereas their rural-living cousins do not. And it is well-known that, historically, food is the main driver of beak size and shape in Darwin’s finches.

When genetic analyses were conducted later in the lab, the research team found few genetic mutations in the genes encoding these measured traits in rural and urban representatives of both species, and none of those mutations were consistent. Since recent work showed that changes in the copy number of genes is linked to rapid evolution in pepper moths and in primates, Ms. McNew and her team looked to see whether differences in gene copy number may explain the measured differences between urban and rural populations of these two finch species. Once again, they uncovered no fixed differences in gene copy numbers between the urban and rural populations for either species.

“There’s been some evidence that certain genetic markers underlie variation in beak size and shape, but overall Geospiza finches are very difficult to distinguish genetically,” Ms. McNew said. “Could there be another source of phenotypic variation?”

When the team looked at epigenetics, they found a significant number of differences between urban and rural finches of both species.

“In the finches that we studied, epigenetic alterations between the populations were dramatic, but minimal genetic changes where observed,” said the study’s senior author, biologist Michael Skinner, a professor at Washington State University. Professor Skinner’s lab conducted the genetic and epigenetic analyses for this study.

The team also found these epigenetic differences were species-specific: few were shared between medium and small ground finches, in spite of their close family ties. This suggests that medium and small ground finches are each responding rapidly and in their own unique ways to environmental changes at the urban site.

Many of these observed epigenetic changes were associated with genes involved in metabolism and in intercellular communications. Other epigenetic mutations were associated with genes related to beak size and shape. These changes make intuitive sense in view of the fact that the diet of urban finches is diverging away from that consumed by rural populations.

“These species of finch have distinct diets which could explain the differences in methylation patterns as diet is known to influence epigenetics,” Professor Skinner said."

My comment: Scientists begin to understand the reasons why organisms are capable of adapting so rapidly to changing environment. Scientists themselves admit that the traditional bumper sticker, random mutations and selection doesn't explain the rapid and effective adaptation and variation of organisms. Rapid changes are caused by epigenetic mechanisms driven by nutrition, climate, stress factors, environmental toxicants, etc. Random mutations and selection have nothing to do with these ingenious mechanisms. The most common epigenetic mechanisms are DNA methylation, histone markers, and information transmitted by non-coding RNA molecules.

Epigenetic information layers are inherited, according to researchers. The study also confirms that changes in epigenetic information structures may also result in alterations in the DNA sequence. However, researchers did not find any consistent links between sequence changes and morphological changes experienced by birds. It is, therefore, clear that genetic defects in the modification of epigenetic information layers will occur in the DNA. Gradually, the genome of all organisms is degenerated and degraded. No new biological information will be added. All changes in organisms are based on epigenetic regulation of existing biological information or loss of information. Therefore there is no mechanism for evolution. Don't get lost.