Dinosaurs to Birds - an open question

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Post-Darwinian genomics has challenged the birds-from-dinosaurs hypothesis in a number of ways. For example, some studies have found that birds and dinosaurs share fewer genetic similarities than previously thought. Additionally, some studies have found evidence that birds may have evolved from a group of reptiles called archosaurs, rather than from dinosaurs.

One of the most significant challenges to the birds-from-dinosaurs hypothesis came from a study published in the journal Science in 2014. In this study, researchers analyzed the genomes of 48 different species of birds and dinosaurs. They found that birds shared fewer genetic similarities with dinosaurs than with other reptiles, such as crocodiles and lizards.

This finding suggests that birds and dinosaurs may not be as closely related as previously thought. 

Another challenge to the birds-from-dinosaurs hypothesis comes from the fossil record. The fossil record is the only direct evidence of past life, and it can be used to track the evolution of different species. However, the fossil record of birds and dinosaurs is incomplete. There are many gaps in the fossil record, and these gaps make it difficult to determine the exact relationships between different species.

For example, there is no fossil evidence of a transitional form between birds and dinosaurs. A transitional form is a species that has some of the characteristics of both birds and dinosaurs. The lack of a transitional form suggests that the evolution of birds from dinosaurs may not have happened.

The presence of junk DNA and horizontal gene transfer (HGT) can complicate the task of inferring evolutionary relationships between organisms, including birds and reptiles.

Junk DNA, also known as non-coding DNA, comprises a significant portion of the genome that does not directly code for proteins. While its function is not fully understood, it is believed to play a role in gene regulation, chromosome structure, and other cellular processes. However, the presence of junk DNA can make it challenging to identify homologous sequences, which are DNA sequences that share a common ancestor. This can, in turn, make it difficult to construct accurate phylogenetic trees, which represent the evolutionary relationships between different species.

Horizontal gene transfer (HGT) is the movement of genetic material between organisms that are not parent and offspring. This process can occur through various mechanisms, such as viral infection or bacterial conjugation. HGT can introduce genes into an organism's genome that are not shared with its closest relatives. This can distort the pattern of shared genes, making it more difficult to infer evolutionary relationships.

In the case of birds and reptiles, the presence of junk DNA and HGT has led to debate about their evolutionary relationship. The presence of junk DNA and HGT has made it difficult to resolve this debate definitively.

In addition Non-neutral synonymous mutations makes it difficult to show that birds have a common ancestor with reptiles. This is because synonymous mutations, which are mutations that do not change the amino acid sequence of a protein, can still have an effect on the fitness of an organism. For example, synonymous mutations can change the folding of the mRNA molecule, which can affect the efficiency of translation. Additionally, synonymous mutations can change the binding sites of regulatory proteins, which can affect the expression of the gene. As a result, synonymous mutations can contribute to the genetic divergence between species, making it more difficult to determine their evolutionary relationships.

GC bias, codon bias, and AT mutation bias makes it challenging to show that birds have a common ancestor with reptiles. These biases can lead to differences in the DNA sequences of birds and reptiles, even if they share a common ancestor.

  • GC bias is the tendency for certain DNA sequences to have a higher proportion of guanine (G) and cytosine (C) nucleotides than others. This bias can be caused by a number of factors, including the activity of transposable elements and selection for certain codon usage patterns.

  • Codon bias is the non-random use of synonymous codons, which are codons that code for the same amino acid. Codon bias can be caused by a number of factors, including the availability of different tRNA molecules and the efficiency of different codons in translation.

  • AT mutation bias is the tendency for DNA sequences to mutate more frequently from AT to GC nucleotides than from GC to AT nucleotides. This bias is thought to be caused by the spontaneous deamination of cytosine to uracil, which can then be misread as thymine by DNA polymerase.

These biases can make it difficult to reconstruct the evolutionary relationships between different species, including birds and reptiles. For example, if two species have different GC contents, it may be difficult to determine whether this is due to a common ancestor or to independent evolution. Similarly, if two species have different codon usage patterns, it may be difficult to determine whether this is due to a common ancestor or to different selective pressures.

In short the more we know the less we know, especially with common ancestry.

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