Incomplete Lineage Sorting: A Major Source of Gene Tree Discordance in UCEs


Ultraconserved elements (UCEs) are stretches of DNA that are highly conserved across species, making them valuable markers for phylogenetic studies. However, despite their high conservation, UCEs can still exhibit gene tree discordance, where the evolutionary history of a particular UCE differs from the overall species tree. Recent research has identified incomplete lineage sorting (ILS) as a major contributor to this discordance.

Understanding Incomplete Lineage Sorting

ILS occurs when ancestral genetic polymorphisms persist through multiple speciation events. This means that different alleles of a gene may be inherited by different descendant species in a way that does not reflect the true species relationships. Imagine a population with two alleles for a particular gene, 'A' and 'B'. If this population splits into two species, it's possible that one species might inherit only allele 'A' while the other inherits only allele 'B'. This can lead to a gene tree that suggests these two species are more closely related than they actually are, simply because they share a common allele.

The Impact of ILS on UCEs

UCEs, despite their high conservation, are not immune to ILS. In fact, studies have shown that ILS can be a significant source of gene tree discordance in UCE datasets. This is because UCEs, like any other genetic loci, are subject to the same evolutionary processes, including genetic drift and mutation. Even though UCEs evolve more slowly than other regions of the genome, they can still accumulate mutations and experience ILS over long periods.

Factors Contributing to ILS in UCEs

Several factors can contribute to the prevalence of ILS in UCEs:

  • Short branch lengths: UCEs tend to have short branch lengths in phylogenetic trees due to their slow evolutionary rate. This can make it difficult to resolve relationships between closely related species, increasing the likelihood of ILS.

  • Large effective population sizes: ILS is more likely to occur in species with large effective population sizes. This is because genetic drift, which can eliminate ancestral polymorphisms, is weaker in larger populations.

  • Rapid speciation events: When speciation events occur rapidly, there is less time for ancestral polymorphisms to be sorted out, increasing the chance of ILS.

Implications for Phylogenetic Studies

The prevalence of ILS in UCEs has important implications for phylogenetic studies. It means that relying on a single UCE tree may not accurately reflect the true species relationships. To overcome this challenge, researchers often use multiple UCEs and employ methods that account for ILS, such as coalescent-based approaches. These methods can help to resolve species relationships more accurately by considering the possibility of gene tree discordance due to ILS.

Conclusion

Incomplete lineage sorting is a major factor contributing to gene tree discordance in UCEs. Understanding the role of ILS is crucial for accurately reconstructing species relationships using UCE data. By employing appropriate phylogenetic methods and considering the potential impact of ILS, researchers can gain a more accurate picture of evolutionary history.


Link


 

Comments

Post a Comment

Popular posts from this blog

Natural Selection has not been accurately measured since Darwin

Image
Francis Crick's term "frozen accident" falsely described the seeming rigidity of the genetic code, its apparent inability to accommodate additional amino acids beyond the standard 20. This observation had puzzled scientists for decades, as the genetic code seems to have reached a plateau in its expansion despite the potential for incorporating new amino acids with novel properties. NeoDarwinian thinking reasoned greater natural selection could occur with more codons. Several hypotheses were put forward to explain this apparent standstill in the genetic code's evolution. Crick and others  eventually applied natural selection to think redundant codons were neutral as to account for neutral selection . The question of why the genetic code stopped incorporating new amino acids remained a fascinating topic in evolutionary biology till Cas9 Crispr. The redundancy of codons, where multiple codons can specify the same amino acid, has long been considered a neutr
Read more

The Origin at 150: Charting a New Evolutionary Voyage on Post-Genomic Seas

Image
“The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.” -EV Koonin, cited by over 250,000 scientists. The Origin at 150: Charting a New Evolutionary Voyage on Post-Genomic Seas As the 150th anniversary of Charles Darwin's epochal "On the Origin of Species" casts a long shadow, evolutionary biologist Eugene V. Koonin throws down a gauntlet in his essay "The Origin at 150: Is a new evolutionary synthesis in sight?" He contends that the Modern Synthesis, the reigning framework since the 1950s, has crumbled under the weight of post-genomic discoveries. This audacious claim compels us to ask: has the ship of evolutionary understanding truly run aground, and if so, can a new v
Read more

Developmental Plasticity: A Worm's Eye View

Image
Imagine a world where your genes don't dictate your destiny. This isn't science fiction; it's the remarkable reality of developmental plasticity. While the blueprint of life lies within our genes, the environment can sculpt and refine that blueprint, shaping who we become. To understand this fascinating concept, let's shrink ourselves down to the size of a worm, in this case, the transparent roundworm Caenorhabditis elegans (C. elegans). These millimeter-long marvels hold the key to unlocking the secrets of developmental plasticity. C. elegans boasts a mere 1031 cells, each with a predetermined fate – or so we once thought. These worms develop in a remarkably consistent manner, following a precise cell lineage. However, this seemingly rigid program belies a surprising level of flexibility. Environmental cues, like temperature or food availability, can trigger dramatic changes in their development. For instance, when faced with limited food, C. elegans can en
Read more