Incomplete Lineage Sorting points away from deep common ancestors to recent bottleneck during Noah

The paper "Pervasive incomplete lineage sorting illuminates speciation and selection in primates" published in the journal Science in 2022 investigated the extent of incomplete lineage sorting (ILS) in the genomes of primates. ILS is a phenomenon in population genetics where ancestral gene copies fail to coalesce (merge) into a common ancestral copy until deeper than previous speciation events. This can happen when speciation events occur relatively quickly, or when the population size is small.

The authors of the paper found that ILS was pervasive in primate genomes, affecting up to 64% of the genome at individual nodes. They also found that ILS was more common on the X chromosome than on autosomes, and that it was more common in genes with immune functions than in housekeeping genes.

The authors used ILS to reconstruct speciation times and ancestral population sizes in primates. They found that speciation times were much more recent than genomic divergence times. They suggest that speciation in primates occurred more rapidly than previously thought.

Here are some of the key takeaways from the paper:

  • ILS is pervasive in primate genomes, affecting up to 64% of the genome at individual nodes.

  • ILS is more common on the X chromosome than on autosomes, and it is more common in genes with immune functions than in housekeeping genes.

  • ILS can be used to reconstruct speciation times and ancestral population sizes in primates.

  • Speciation times in primates were much more recent than genomic divergence times pointing to a bottleneck event.

All humans may be descended from just TWO people and a catastrophic event almost wiped out ALL species 100,000 years ago,study suggests.

Research prompted speculation humans and animals sprang from single pairs.

This may have happened after a catastrophic event after the last ice age.

A scientific study has prompted speculation that all modern humans could have descended from a solitary pair who lived 100,000 years ago.

Scientists surveyed the genetic 'bar codes' from 100,000 different species and the results have prompted speculation that we sprang from a single pair of adults after a catastrophic event almost wiped out the human race.

'This conclusion is very surprising,' Thaler admitted, 'and I fought against it as hard as I could.' 

The conclusions throw up considerable mystery as to why the need for human life to start again was needed such a relatively short time ago, especially since the last known extinction we know of was during the time of the dinosaurs 65 million years ago.

One might have thought that, due to their high population numbers and wide geographic distribution, humans might have led to greater genetic diversity than other animal species,' added Stoeckle.

https://www.biorxiv.org/content/10.1101/276717v2

ILS can happen due to Bottlenecks. A bottleneck is a sudden reduction in the size of a population. This can happen due to a number of factors, such as a natural disaster. Bottlenecks can lead to the loss of genetic diversity, which can increase the likelihood of ILS.

Incomplete lineage sorting (ILS) can happen when the effective population size (Ne) is small, such as on the X chromosome.

In this study the authors found that the levels of ILS on the X chromosome were lower than expected under neutral evolution. This suggests that the effective population size of the X chromosome was even smaller than expected, which could be due to a population bottleneck.

The study suggest that the low levels of ILS on the X chromosome in primates are likely due to a population bottleneck that occurred in the past.

The study provides further evidence that population bottlenecks can have a significant impact on the genetic diversity of a population.

The paper is available to read at the following link: https://science.sciencemag.org/doi/10.1126/science.abn4409





Comments

Post a Comment

Popular posts from this blog

Beyond the Sequence: The Epigenetic "Fingers" That Play the DNA Keyboard

Image
Imagine the keyboard itself is not a standard piano keyboard, but a modular synthesizer, capable of producing an almost infinite array of sounds. The DNA sequence, then, represents the fundamental building blocks of this synthesizer, the raw materials from which all sounds are generated. Epigenetics, our "fingers," manipulates these building blocks, adjusting parameters like volume, timbre, and rhythm, transforming the raw potential of the DNA sequence into a symphony of cellular functions. We can further refine the "fingers" analogy. Consider that each finger represents a distinct epigenetic mechanism: DNA methylation, histone modifications, and non-coding RNA.  DNA methylation, for instance, might be the "index finger," capable of precisely silencing specific genes, like muting individual keys on the synthesizer. Histone modifications, the "middle finger," could represent the ability to adjust the accessibility of the DN...
Read more

Why are Christian philosophers running towards Darwin while biologists are "running" away?

Image
As nature reveals the strength of epigenetics and the weakness of Neo-Darwinism, biologists are “running” away from the long-standing accepted theory. In The Federalist , April 2019, Benjamin Dierker reviews “Why one-third of biologists now question Darwinism”: "Current estimates are that approximately one-third of professional academic biologists who do not believe in intelligent design find Darwin’s Theory inadequate to describe all of the complexity in biology.” Dierker continues, “The important note is that these are not ideologues or religious zealots, nor do they propose a god or biblical solution.  Rather, they find problems in the lack of explanatory power of Darwin’s theory in light of modern understanding of mutation, variation, DNA sequencing and more. These expressions of doubt do not reject naturalism or evolution per se, but the rigor of the Neo-Darwinian model for explaining the development of life.” For 40 years, scientists calculated natural se...
Read more

Rewriting the Rules: Epigenomic Mutation Bias Challenges Randomness in Evolution

Image
This research challenges the long-held dogma that mutations occur randomly, irrespective of their consequences, by demonstrating a clear, epigenome-mediated mutation bias in Arabidopsis thaliana . The study meticulously unveils how mutation rates are not uniform across the genome but are significantly reduced in functionally constrained regions, particularly within gene bodies and essential genes. This discovery fundamentally alters our understanding of evolutionary processes, suggesting that mutation is not a purely directionless force. "Mutation bias reflects natural selection in Arabidopsis thaliana" This opening statement encapsulates the core finding: mutation rates are not random but reflect epigenetic pressures. The authors demonstrate that mutations are less frequent in crucial genomic regions, directly contradicting the prevailing theory of random mutation. This observation suggests an active mechanism that minimizes deleterious mutations in essentia...
Read more