How Can We Determine if Evolution is Driven by Selection or Genetic Drift?

[windy miller]

As I understand it , evolutionary change can be caused via selection effect or through genetic drift. are there any formal test for which is the dominant machismo for a given trait?
A related question, is, we have lots of evidence that species evolve via nested hierarchy , but how can test if that descent with modification and common ancestry happened through natural selection or some other mechanism?

 

[Evo]

A related question, is, we have lots of evidence that species evolve via nested hierarchy , but how can test if that descent with modification and common ancestry happened through natural selection or some other mechanism?

No, we cannot test for these things. We just know that there has not been the technology before to selectively do selective genetic modification on a worldwide scale. Any other questioning would wander into conspiracy theory.

 

[windy miller]

So what about papers like this:
https://www.annualreviews.org/doi/pdf/10.1146/annurev-genet-111212-133526
and this:
https://www.ncbi.nlm.nih.gov/pubmed/9691061
?

 

[BillTre]

There are methods that can test for the results of a selective sweep.
This occurs only sometimes when an identified change is strongly selected for in the right kind of genetic background.
What is detected is a reduced amount of genetic variability in the molecular neighborhood of the under selection.
The idea scenario for detection would be something like:
Population with a bunch of genetic variability distributed throughout its genome.

• A new strongly selected mutation arises, once, in a neighborhood of the genome with numerous genetic markers distinct from those of similar neighborhoods in other individuals of the population. Thus, not only is the adaptive mutation different, but several nearby genetic markers are distinct from others in the population.
  
• Selection will promote the positive mutation to the next generation. The rest of the genome will be unaffected by this selection (because they are randomly sorted with respect to the adaptive genes presence) except those parts of the genome nearby (or tightly linked to in genetics terminology) the mutation. They will be "dragged along" through meiosis by their linkage to the gene and then benefit from the adaptive selective value of their linked neighboring gene.

The closer a marker is linked to an adaptive gene, the less likely it is to be exchanged during crossing over (recombination) during meiosis.
Crossing over is the most common way these tightly linked markers could be separated from the adaptive gene.
The likelihood of a crossover happening would be represented by its genetic map distance, which is the percentage of times a crossover happens between two genes or markers when it goes through meiosis. This can be below 1%. It can take a lot of generations to separate closely linked markers.

 

[Ygggdrasil]

In addition to the methods mentioned by Bill, researchers can also assess selection for particular genes by examining the dN/dS ratio (also referred to as the Ka/Ks ratio): https://en.wikipedia.org/wiki/Ka/Ks_ratio

Essentially, the method looks at the frequency of non-synonymous mutations (mutations that change one amino acid to another) versus synonymous mutations (mutations that do not affect the amino acid sequence of the resulting protein). The synonymous mutations are assumed to be neutral, whereas at least some of the non-synonymous mutations could have a fitness effect. An excess of non-synonymous mutations over synonymous mutations suggests that some of those mutations are undergoing positive selection (the mutations confer a fitness benefit, causing the mutations to rapidly spread throughout the population), whereas a low rate of non-synonymous mutations would suggest purifying selection (mutation to the gene is deleterious to fitness, so mutations are strongly selected against).

As with most things in science, there is no one definitive test of whether a particular trait evolved under selection or neutral drift. Rather, one must build a case by looking at a variety of different sources of evidence, not just those based on DNA sequence analysis, but also experimental data testing the effects of particular genes and mutations (e.g. see this nice paper that uses experimental studies in mice to build the case for positive selection of a mutation among Asian populations: https://www.cell.com/cell/fulltext/S0092-8674(13)00067-6). The review you cite from Pardis Sabeti would be a good source to consult, as she is one of the experts at the forefront of this field.

No, we cannot test for these things. We just know that there has not been the technology before to selectively do selective genetic modification on a worldwide scale. Any other questioning would wander into conspiracy theory.

There are certainly mechanisms that contribute to evolution beside natural selection. Some believe that these mechanisms, such as genetic drift, may contribute to many more of the genetic changes we see throughout evolution than natural selection: http://discovermagazine.com/2014/march/12-mutation-not-natural-selection-drives-evolution As discussed in Bill's and my post, scientists have devised (and are continuing to work on) methods to test whether certain genes/mutations are under selection.

Distinguishing between mutations that spread via positive selection versus neutral drift mechanisms is not only important in evolutionary biology, but also in cancer biology. Tumors accumulate mutations over time and some of these mutations (called as driver mutations) contribute to carcinogenesis. At the same time, other mutations are also occurring in the tumor cells (called passenger mutations) that do not appreciably affect carcinogenesis. When studying the mutations found in tumors, researchers have put a lot of effort into disentangling the driver mutations from the passenger mutations in order to figure out what genes and biological pathways are contributing to the growth and proliferation of particular cancer types.

 

[windy miller]

thanks guys that's very helpful

 

[Evo]

thanks guys that's very helpful

Sorry, I thought the question was could we test for intentional genetic modification as opposed to natural occurances. I should have clarifed instead of "assuming". My mistake.

 

[Ygggdrasil]

Quanta magazine published a nice article on the topic of natural selection vs neutral drift in evolution: https://www.quantamagazine.org/neut...enged-by-evidence-for-dna-selection-20181108/