Common Ancestry and Junk DNA via HGT in the Light of the Extended Evolutionary Synthesis

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“When thinking about genetics, we often think of lineages and the passing down of genes through generations. We think about {neo darwinian} vertical transmission. However, bacteria also acquire genetic material through horizontal transmission {HGT}. The human body is a complex biological network comprising ten microbes for each human cell and 100 microbial genes for each unique human gene”. Understanding bacterial networks of gene exchange is thus essential for an understanding of ourselves.” - Nature


Common Ancestry and Junk DNA via HGT in the Light of the Extended Evolutionary Synthesis

The field of ancestral studies has undergone a fascinating shift in recent decades. Exonic DNA, which codes for proteins, was once the primary focus. However it only mades up 2% of the DNA so to conclude we shared 98% of our genes with chimpanzees was to conclude we shared 98% of only 2%,  hardly an accurate comparison of ancestry.


Percentage of human shared exonic DNA with different animals.

Researchers are now turning to the vast realm of non-coding, or "Junk," DNA for insights into our shared past.

However, horizontal gene transfer (HGT), the phenomenon where genetic material hops between species, adds a layer of complexity to using junk DNA for ancestry studies. Unlike exonic DNA, which is usually tightly constrained by its role in protein synthesis, Junk DNA can be more fluid and susceptible to HGT. This makes it tricky to disentangle ancestral inheritance from horizontal acquisitions.

HGT also offers intriguing possibilities. Studying how genes move between species can shed light on ancient evolutionary processes and adaptations. For example, some researchers believe HGT may have played a crucial role in the development of antibiotic resistance in bacteria as well as the placenta.

Using junk DNA for ancestry studies requires careful consideration of HGT. 

Ultimately, the story of our shared ancestry is likely a complex tapestry woven from both vertical inheritance and horizontal transfer. By embracing the challenges and opportunities presented by junk DNA, we can gain a deeper and more fascinating understanding of the intricate web of life that binds us all.

Horizontal gene transfer (HGT) in junk DNA can significantly obscure the relationships between organisms in ancestral studies. Here's a closer look at how it happens:

Challenges Introduced by HGT:

  • Masking Ancestral Signals: Junk DNA, despite its name, plays important roles in gene regulation and other cellular processes. When genes are transferred horizontally, they can disrupt existing genetic relationships and make it harder to trace ancestral lineages. This is because the transferred genes may not have been inherited vertically from a common ancestor, blurring the evolutionary signal.

  • Convergent Evolution: HGT can lead to similar traits evolving independently in different lineages through the acquisition of the same genes. This can create false phylogenetic signals, making it appear as though organisms are more closely related than they actually are.

  • Incomplete Lineage Sorting: Sometimes, genes acquired through HGT may be retained in multiple lineages for a long time before eventually being lost. This can further complicate ancestral reconstruction, as it can be difficult to determine whether shared genes are due to common ancestry or horizontal transfer.

Consequences for Ancestral Studies:

  • Less Accurate Phylogenetic Trees: Traditional methods for reconstructing evolutionary relationships may be misled by HGT, leading to inaccurate phylogenetic trees that don't reflect the true history of life.

  • Difficulty Identifying Ancestral Populations: Distinguishing between ancestral inheritance and HGT can be challenging, making it difficult to pinpoint the origins of specific populations and their evolutionary trajectories.

  • Limited Understanding of Trait Evolution: If traits are acquired through HGT, it becomes harder to understand how they evolved and spread within lineages. This can hinder our understanding of the diversification and adaptation of life.

While HGT undoubtedly complicates ancestral studies, it also offers fascinating insights into the interconnectedness of life and the dynamic nature of evolution. By acknowledging its challenges and developing new analytical tools, researchers can continue to unravel the mysteries of our shared past, even in the face of the "messy" signals found in junk DNA.

Horizontal gene transfer (HGT) in non-coding DNA can poses challenges to the interpretation of evolutionary relationships within the framework of neo-Darwinism. Here's how:

Challenges to Phylogenetic Trees:

  • Blurred Lines: Traditional NeoDarwinian phylogenetic trees rely on the assumption that genes are inherited vertically from ancestors. However, HGT introduces "horizontal branches" that disrupt this linear descent, making it harder to accurately reconstruct evolutionary history. 

Phylogenetic representation of the "Bush of Life"

Verses Darwins "Tree of Life"


This can lead to misinterpretations of relationships between organisms, potentially placing them in the wrong branches or even entirely different clades.

  • Convergent Evolution Mimics: HGT can also lead to convergent evolution, where unrelated organisms acquire the same genes through horizontal transfer, making them appear more closely related than they actually are. This can be particularly misleading in cases where the transferred genes are involved in similar functions or adaptations.

Challenges to Selection:

  • Unclear Selective Pressures: Neo-Darwinism emphasizes natural selection acting on individual organisms and their genes. However, HGT introduces a scenario where genes can "jump ship" between species, potentially escaping the selective pressures they originally faced. This makes it harder to understand how selection has shaped the evolution of certain traits, especially those encoded in non-coding DNA.

  • Cooperative Evolution: HGT can also facilitate cooperative evolution, where genes interact and benefit each other across species boundaries. This can complicate the picture of "survival of the fittest" at the individual level, as the success of a gene might depend on its interactions with genes in other organisms.

HGT is a complex phenomenon, and its impact on evolutionary relationships varies depending on the specific genes and organisms involved.

Studying HGT can provide valuable insights into the interconnectedness of life and the emergence of novel adaptations.

Therefore, viewing HGT as a challenge to neo-Darwinism, provides a more accurate additional layer of complexity that requires new approaches and interpretations within the broader framework of evolutionary theory. Scientists are actively developing new methods and models to account for HGT and its implications for reconstructing evolutionary history and understanding the mechanisms of selection.

Ultimately, the ongoing dialogue between HGT and neo-Darwinism can lead to a richer and more nuanced understanding of the ever-evolving tapestry of life by moving to an inclusive Extended Evolutionary Synthesis.

Ref:

Evolutionary change and phylogenetic relationships in light of horizontal gene transfer

The modern synthesis in the light of microbial genomics

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