Why the standard definition of evolution fails

In a recent blog Larry Moran wrote:

"Recall that evolution is defined as a change in the frequency of alleles in a population and the main mechanisms of change are natural selection and random genetic drift."

and further:

"Symbiosis is a rare example of substantial change in the frequency of alleles in a population. It helps explain some of the changes we see in the history of life. It does not require a revision of population genetics."

The definition of evolution he uses is very restrictive and out-dated. At the same time it implies that Darwin's Origin of Species was not about evolution. Darwin simply did not know about "a change in the frequency of alleles". Poor Darwin! More importantly, the second quote above demonstrates what the consequences are of such a restricted definition: the outrageous misrepresentation of the eukaryotic endosymbiosis event. It is a gross distortion of what the Eukaryotic symbiosis entails. Endosymbiosis is the permanent incorporation of one complete genome of one species in a single cell of another species resulting in two different genomes in one cell (now called mitochondria and chloroplasts). This event has nothing to do with 'a change in allel frequencies'. This definition of evolution implies that the Eukaryotic symbiosis event is not evolution! However, the Eukaryotic merger is the single most important event in the history of life on Earth. Without it no animals and plants. Without mitochondria and chloroplasts we would not exist. They are crucial. If you stubbornly and dogmatically hold to an outdated definition, it can only result in the distortion of the facts. That is not science. 

There is more. Much more. What about speciation? That is: The Origin of Species! (the title of Darwin's breakthrough work). Speciation is certainly more than 'a change in frequency of alleles in a population'. The theory of evolution should explain why there are species at all. And how they originate. And why they don't merge into one species again ( reproductive isolation ), that is how the separateness and individuality of species is maintained. 

What about genome duplication ( polyploidy )? Polyploidy, or whole-genome duplication, is widespread in the plant kingdom, but also known in animals. Polyploidy occurs in invertebrates and vertebrates: flatworms, fish, amphibians, lizards. Polyploidy has arisen by a variety of mechanisms in a diverse array of animal taxa, covering nearly every major phylum (source). Susumu Ohno proposed that two rounds of polyploidy occurred early in vertebrate evolution (source). If anything is inappropriate to describe polyploidy than is certainly is 'the change of frequency of alleles in populations'.

What about Lateral Gene Transfer? That is:  the transfer of genetic material between organisms other than by the vertical transmission of DNA from parent to offspring. A change of gene frequency? No, it is a sudden increase of the genomic content of an organism.

What about deletions of (large) segments of DNA? What about chromosomal inversions? What about chromosomal translocations? What about chromosomal fusions? Let's focus on an important, but not well-known chromosome fusion in the human lineage. A fusion of two relatively small chromosomes in our ancestors created the human chromosome 2. This resulted in a reduction of the diploid number of chromosomes from 2n=48 to 2n=46 chromosomes. No significant loss of chromosomal material, but a significant event nonetheless. It defines the human species. It separates us from  the apes. 

The origin of chromosome 2 by fusion of two chromosomes (wikipedia)

human chromosome 2 lined up with chimpansee, gorilla, orangutan
For details see blog John Hawks

The diagram shows that the chromosome bands of two different chromosomes of chimpansee, gorilla, and orangutan precisely match human chromosome 2. Strong evidence of a fusion. This couldn't be further removed from 'a change in the frequency of alleles' [2].

What about structural variants in the human genome including cytogenetically detectable and submicroscopic deletions, duplications, large-scale copy-number variants, inversions and translocations? (source). It has been calculated that humans have more than 15,000 duplicated genes [3]. To describe each of them with 'a change of the frequency of alleles' would be a gross distortion. It ignores the creation of new genes.

What about the subject of Larry Moran's book: junk DNA? 90% of Your Genome Is Junk. Can the scandalous accumulation of so much junk DNA in the human genome be described in terms of 'a change of the frequency of alleles'? Which alleles? Anyway, can junk DNA be described in terms of alleles? Junk alleles? How do you define the begin and end of a junk allel? 

Futuyma & Kirkpatric

The definition of evolution in the most recent evolution textbook:

"Biological evolution is inherited change in the properties of groups of organisms over the course of generations". Futuyma and Kirkpatric (2023) page 9.

It's immediately clear that 'alleles' or 'genes' are not mentioned in this definition. It's all about inherited phenotypic properties of groups of organisms [1].

Let me quote the famous evolutionary biologist Ernst Mayr:

"It is simply not true that evolution can be explained as a change in gene frequencies." Mayr points out that this definition fails to explain "the multiplication of species, the origins of evolutionary novelties and higher taxa, and the occupation of new adaptive zones." (Ernst Mayr, William Provine (1998) The Evolutionary Synthesis, Prologue page 12.)

Blindness for chromosomal location of alleles

The definition of evolution as "a change in the frequency of alleles in a population" is blind for the location of an allel on a chromosome. Suppose, a gene moves from chromosome A to chromosome B without changing its sequence. So, there is no change in the frequency of the allel. A population geneticist would not note any difference. A cytogeneticist however would note a difference. This migration of genes from one chromosome to another has happened during evolution of the Y-chromosome. By one estimate, the human Y chromosome has lost 1,393 of its 1,438 original genes over the course of its existence (the wikipedia Y-chromosome page is of high quality). There is evidence that genes located on the Y-chromosome have been relocated to autosomes (source). There is also evidence that during evolution genes moved from mitochondrion to the nucleus. These migrations, although evolutionarily important, do not show up as a change in the frequency of alleles of a species. In fact any change in the chromosome complement of a population or a species (for example a reciprocal translocation) would and could not be noticed as a change in gene frequency. This idea could be further elaborated. [paragraph added 4 Feb 2025] 

Notes

1. This definition is compatible with all chromosomal rearrangements mentioned in this blog because they are inherited. For example, the fusion that created human chromosome 2 is inherited. In a sense it is the phenotype (appearance) of the karyotype. The karyotype is different from the DNA sequence. The karyotype is the way how the total of DNA is distributed over the chromosomes. [6 Feb 2025]
2. A very nice illustration of the role of chromosomes in reproductive isolation see: Rapid chromosomal evolution in island mice, Nature 13 January 2000. [7 Feb 2025]
3. Jianzhi Zhang (2003) Evolution by gene duplication: an update, TRENDS in Ecology and Evolution Vol.18 No.6 June 2003. [7 Feb 2025]