"Junk DNA" causes Reticular Evolution not Darwins March of progress

In an article "Faces of Yesterday" Henry Gee a senior editor of Nature is arguing that the idea of a "missing link" in human evolution is no longer tenable. The author points out that we have a lot of evidence about hominid life from the period when humans started to diverge from apes, and that this evidence does not fit neatly into a linear progression. 


Instead, it suggests that human evolution was a more complex process (reticular), with many different species evolving and interbreeding (introgression) over time.

The author is correct that the idea of a "missing link" is simplistic. Evolution is a complex process, and it's not always possible to neatly fit all of the evidence into a single, linear narrative.

We have fossils of early hominids, we have DNA evidence, and we have archaeological evidence of early human cultures. But how this ties together is still a mystery. The idea of a "missing link" is a useful way to think about human evolution, but it's important to remember that it's just a metaphor. Evolution is a continuous process, and there is no single point at which a "human" suddenly appears.

Neodarwins random mutation can't evolve man fast enough these authors found.

"In this article we apply these results to obtain insights into regulatory sequence evolution in Drosophila and humans.

Durrett and Schmidt (2007) have recently given a mathematical analysis for regulatory sequence evolution in humans

Using a generation time of 25 years, they found that in a 1-kb region, the average waiting time for words of length six was 100,000 years. For words of length eight, they found that the average waiting time was 375,000 years when there was a seven- of eight-letter match to the target word in the population consensus sequence (an event of probability ∼5/16) and 650 million years when there was not.

Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution

10.1534/genetics.107.082610

We should not look at human evolution as retricular not a Darwinian tree


These authors point out:

"Evolution of eukaryotic species and their genomes has been traditionally understood as a vertical process in which genetic material is transmitted from parents to offspring along a lineage, and in which genetic exchange is restricted within species boundaries.

Mounting evidence from comparative genomics indicates that this paradigm is often violated.

Horizontal gene transfer and mating between diverged lineages blur species boundaries and challenge the reconstruction of evolutionary histories of species and their genomes.

A paradigm shift is needed to naturally accommodate non vertical processes in eukaryotic evolution.

Reticulated evolution—also known as network evolution or non vertical inheritance—refers to the total or partial merging of genetic material between two diverged lineages, leading to evolutionary histories that are better depicted by a phylogenetic network than by a steadily bifurcating tree.

Recent genomic research has brought reticular evolution to the forefront of eukaryotic genome evolution.

Importantly, processes of nonvertical evolution can be the source of incongruence among phylogenetic trees constructed from different genes in a genome.

The emerging picture is complex and fragmented, and there is a need to assess global patterns that shed light on what factors modulate nonvertical inheritance across the diversity of eukaryotes.

The branching patterns of human, chimpanzee, and gorilla were later shown to be variable across genomic regions.

In the face of disturbing gene incongruence, the assumption of analytical or vertical-evolutionary causes seemed satisfactory, and the quest for phylogenetic relationships among eukaryotes kept an idealized, fully bifurcating tree as a paradigm.

The study of evolution has shown that the probability (NeoDarwinism) of an event is only one of the factors in the interplay of chance and necessity that governs the emergence of new traits

The “you are what you eat” hypothesis, suggested that phagotrophic eukaryotes inevitably accumulate genes acquired from their bacterial prey. And they can enter the human microbiome in the intestines thus to our soma.

Hybridization and introgression at close evolutionary distance: the norm rather than the exception?

Denisovans has provided evidence that ancient hybridization resulted in introgressed regions in different populations of modern humans,

The above observations suggest that gene flux between closely related lineages is likely the norm rather than the exception, and that we need to incorporate this in our interpretation of past events.

Nonvertical evolution, by contrast, introduces the possibility of more radical, nongradual changes in genotypes, resulting in large jumps at both the genotypic and fitness landscapes. Another area of reconsideration is the concept of species. The boundaries should not be assumed to be impenetrable.

Imposing the strong assumption that only vertical processes are in place will, I believe, slow down reconstruction of ancestral genomes and how they evolved.

28 August 2020

Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift

https://doi.org/10.1111/nyas.14471

In summary, since we rejected "Junk DNA" for 30 years we lost out on how this DNA "jumps" about to cause reticular evolution all this time. 


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