New discoveries challenge common ancestry

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Actual phylogenetic "Bush of Life." There is no longer a Darwinian tree of life.

""If "the sublime author of the universe" can create all the different species by separate acts of creation, he can so too, surely create one or two species to begin with, and confer upon them the power of evolving into the rest."

-Jean Baptiste Lamarck, first to describe epigenetics

Phylogenetic's of common ancestry is the belief that all living organisms share a common ancestor.  However, there are a number of factors that can frustrate phylogenetic common ancestry, including biased gene conversion, GC bias (gBGC), codon bias, nonneutral synonymous substitution, AT mutation bias, and horizontal gene transfer of transposable elements (HGT of TEs).

How these factors frustrate phylogenetic common ancestry assumptions:

Biased gene conversion (BGC) is a recombination-associated process that favors the fixation of one allele over another, regardless of its effects on fitness. As such it is not a part of NeoDarwinism. In GC-biased gene conversion (gBGC), the favored allele is usually a guanine or cytosine (GC) base. GC bias can be caused by a number of factors, including the preferential repair of GC base mismatches and the higher recombination rates in GC-rich regions of the genome. 

gBGC is a specific type of BGC that leads to GC bias.

gBGC can frustrate phylogenetic common ancestry in a number of ways. First, it can lead to the accumulation of GC-rich regions in the genome, which can obscure the relationships between species. Second, gBGC can lead to homoplasies, which are shared traits that have developed independent from Darwin in different lineages. This can make it difficult to reconstruct the true history of a group of species.

Here are two specific examples of how gBGC can frustrate phylogenetic common ancestry:

  • GC-rich regions can obscure phylogenetic relationships. GC-rich regions of the genome tend to change more quickly than AT-rich regions. This is because GC-rich regions have higher recombination rates and are more prone to gBGC. As a result, GC-rich regions can accumulate mutations that obscure the true relationships between species. For example, two species that are closely related may have very different GC-rich regions of their genomes, making it difficult to infer common ancestry.

  • gBGC can lead to homoplasies. Homoplasies are shared traits that have developed independently (without Darwin) in different lineages. gBGC can lead to homoplasies by increasing the probability of GC-rich alleles being fixed in multiple lineages. For example, two species that are not closely related may have similar GC-rich regions of their genomes due to gBGC. This can make it difficult to reconstruct the true history of a group of species.

gBGC can have a significant impact on the change of genomes and the reconstruction of phylogenetic relationships. gBCG is a natural cellular process and is not the result of NeoDarwinian mutations.

Codon bias is a phenomenon in which some codons are used more frequently than others in a given gene or genome. It is largely caused by GC bias.

Codon bias can frustrate phylogenetic common ancestry in a number of ways. First, it can lead to the accumulation of synonymous mutations, which are changes to the DNA sequence that do not change the amino acid sequence of the protein. Synonymous mutations can accumulate rapidly in codon-biased genes, which can make it difficult to reconstruct the relationships between species.

Second, codon bias can lead to homoplasies, which are shared traits that have arisen independently in different lineages. This is because codon bias can increase the probability of certain codons being fixed in multiple lineages. For example, two species that are not closely related may have similar codon bias patterns due to independent NonDarwinian evolution. This can make it difficult to reconstruct the true history of a group of species.

Codon bias is a natural mechanism that can have a significant impact on the change of genomes and the reconstruction of phylogenetic relationship.

Nonneutral synonymous substitutions are synonymous substitutions that have a measurable impact on the "fitness" of an organism. 

For 60 years scientists thought they were neutral with no effect on fitness due to NeoDarwinian doctrine. They based their measurement of natural selection (e.g. Ka/Ks) on them in 30,000 articles spanning from the early seventies to today. Recent studies using mutation libraries generated by Cas9 Crispr has challenged this NeoDarwinian axiom.

They can occur in codon-biased genes, where the frequency of certain codons is higher than others. Nonneutral synonymous substitutions can frustrate phylogenetic common ancestry in a number of ways.

First, they can lead to the accumulation of synonymous mutations that are not neutral, which can make it difficult to reconstruct the relationships between species. This is because nonneutral synonymous substitutions can have an impact on NonDarwinian fitness. 

As a result, they can accumulate more quickly than neutral synonymous substitutions, and they can obscure the true relationships between species.

Second, nonneutral synonymous substitutions can lead to homoplasies, which are shared traits that have evolved independently in different lineages. This is because nonneutral synonymous substitutions can be fixed in multiple lineages, even if they are not closely related. This can make it difficult to reconstruct the true history of a group of species.

Here are two specific examples of how nonneutral synonymous substitutions can frustrate phylogenetic common ancestry:

  • Accumulation of non-neutral synonymous mutations. A study of yeast genes found that codon-biased genes accumulated non-neutral synonymous mutations at a rate that was five times higher than non-codon-biased genes. This suggests that nonneutral synonymous substitutions can lead to the rapid accumulation of synonymous substitutions, which can make it difficult to reconstruct the relationships between species.

Nonneutral synonymous substitutions are a natural mechanism that can have a significant impact on the change of genomes and the reconstruction of phylogenetic relationships.

AT mutation bias is a phenomenon in which DNA sequences tend to accumulate adenine (A) and thymine (T) mutations more frequently than guanine (G) and cytosine (C) mutations. This can be caused by a number of factors, including the chemical instability of GC base pairs due to epigenetic methylation of Cytosine and their spontaneous deamination to Thymine and the preferential repair of AT mismatches. As such it is a natural mechanism.

AT mutation bias can frustrate phylogenetic common ancestry in a number of ways. First, it can lead to the accumulation of AT-rich regions in the genome, which can obscure the relationships between species. This is because AT-rich regions tend to change more quickly than GC-rich regions, and they are also more prone to AT mutation bias. As a result, AT-rich regions can accumulate mutations that obscure the true relationships between species.

Second, AT mutation bias can lead to homoplasies, which are shared traits that have arisen independently apart from Darwin in different lineages e.g. bat vs bird wings. This is because AT mutation bias can increase the probability of AT-rich alleles being fixed in multiple lineages. For example, two species that are not closely related may have similar AT-rich regions of their genomes due to AT mutation bias. This can make it difficult to reconstruct the true history of a group of species.

Here are two specific examples of how AT mutation bias can frustrate phylogenetic common ancestry:

  • Accumulation of AT-rich mutations in AT-rich regions. A study of mammalian genomes found that AT-rich regions accumulated AT-rich substitutions at a rate that was five times higher than GC-rich regions. This suggests that AT mutation bias can lead to the rapid accumulation of AT-rich mutations in AT-rich regions, which can make it difficult to reconstruct the relationships between species.

  • Fixation of AT-rich alleles by AT mutation bias. A study of bacteria found that AT mutation bias was responsible for a significant number of homoplasies in the bacterial phylogeny. This suggests that AT mutation bias can make it difficult to reconstruct the true history of bacteria.

AT mutation bias is a natural mechanism that can have a significant impact on the change of genomes and the reconstruction of phylogenetic relationships. 

Horizontal gene transfer (HGT) of transposable elements (TEs) can frustrate phylogenetic common ancestry in a number of ways.

  • TEs can obscure the relationships between species. TEs can move between species and even between kingdoms of life. This can lead to the accumulation of TEs in the genomes of species that are not closely related. As a result, TEs can obscure the true relationships between species.

  • TEs can lead to homoplasies. HGT of TEs can increase the probability of TEs being fixed in multiple lineages. For example, two species that are not closely related may have similar TEs in their genomes due to HGT. This can make it difficult to reconstruct the true history of a group of species.

  • TEs can disrupt genes and cause mutations. TEs can insert themselves into genes and disrupt their function. They can also cause mutations in genes. This can lead to  new traits, but it can also obscure the true relationships between species.

Here are two specific examples of how HGT of TEs can frustrate phylogenetic common ancestry:

  • A study of bacteria found that HGT of TEs was responsible for a significant number of homoplasies in the bacterial phylogeny. This suggests that HGT of TEs can make it difficult to reconstruct the true history of bacteria.

  • A study of plants found that HGT of TEs was responsible for the development of a new gene that is involved in resistance to herbicides. This suggests that HGT of TEs can lead to the the adaptation of new traits, but it can also obscure the true relationships between species.

HGT of TEs is a complex phenomenon with a number of important implications.

HGT of TEs is a powerful natural force that can have a significant impact on the  genomes and the reconstruction of phylogenetic relationships.

Here is a list of other factors that challenge phylogenetic construction of common ancestry, apart from the factors mentioned above:

  1. Incomplete fossil record: The fossil record is incomplete and fragmentary, and it is often difficult to determine the relationships between fossils.

  2. Hybrids and introgression: Hybrids and introgression can mix up the genetic data of different species, making it difficult to reconstruct their relationships.

  3. Reversals: Traits can sometimes be lost or reversed over time, making it difficult to determine the relationships between species.

  4. Long branch attraction: Long branch attraction is a statistical artifact that can cause distantly related species to appear more closely related than they actually are.

  5. Model uncertainty: Phylogenetic trees are constructed using mathematical models, and different models can produce different results. It can be difficult to determine which model is the most accurate.

  6. Data quality: The quality of the data used to construct phylogenetic trees can vary widely. Poor quality data can lead to inaccurate results.

  7. Limited taxon sampling: Phylogenetic trees are only as good as the data they are based on. If the data only includes a small subset of the species in a group, the tree may not be accurate.

  8. Computational limitations: Phylogenetic analysis can be computationally expensive, especially for large datasets. This can limit the accuracy and resolution of phylogenetic trees.

  9. Subjective interpretation: Phylogenetic analysis can be subjective, and different researchers may interpret the data differently. This can lead to conflicting phylogenetic trees.

It is important to note that these are just a few of the many factors that can challenge phylogenetic construction. Most factors are naturally occurring mechanisms that do not rely on NeoDarwinism. Phylogenetic analysis is a complex and challenging field, and there is no single "correct" way to construct a phylogenetic tree.

That common ancestry is an overwhelming axiom is being challenged with the study of the mechanisms above.

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