A Critical Appraisal of Rooting Methods in Prokaryotic Gene Families


“Almost all standard phylogenetic methods for reconstructing gene trees result in unrooted trees; yet, many of the most useful applications of gene trees require that the gene trees be correctly rooted.


The field of evolutionary biology heavily relies on phylogenetic analysis to understand the evolutionary relationships between genes and species. Phylogenetic methods typically reconstruct these relationships as unrooted trees, depicting the relative positions of genes but lacking crucial information about the evolutionary direction. This missing piece – the root – hinders our ability to fully grasp how genes have evolved and diversified over time.

This journal article delves into the critical issue of accurately rooting phylogenetic trees, specifically focusing on gene families within prokaryotic organisms.

The Significance of Rooted Trees:

  • Evolutionary Roadmap: A rooted tree acts as a roadmap, pinpointing the ancestral gene and the direction of diversification within the gene family. This knowledge allows us to trace how ancestral genes have evolved into the diverse array of genes seen today, revealing the evolutionary pressures that shaped their functions.

  • Foundation for Applications: Many downstream analyses in evolutionary biology depend on a correctly rooted tree. Estimating evolutionary rates, identifying ancestral genes, and reconstructing the history of gene gains and losses all require a reliable understanding of the evolutionary direction within the gene family.

Challenges of Rooting Prokaryotic Gene Trees:

The article then dissects the limitations of traditional rooting methods when applied to prokaryotic gene families:

  • Outgroup Rooting Roadblock: The conventional outgroup rooting approach relies on identifying an external group that demonstrably diverged before the lineages of interest. However, this method crumbles for gene trees affected by complex evolutionary histories. Horizontal gene transfer (HGT), a phenomenon where genetic material is transferred laterally between organisms, is a major evolutionary force in prokaryotes. HGT disrupts the simple branching patterns assumed by outgroup rooting, making it difficult to accurately identify a suitable outgroup.

  • A Black Box of Accuracy: Despite their widespread use, the accuracy of most rooting methods remains largely unknown. The lack of systematic evaluations using simulated data sets makes it challenging to gauge their strengths and weaknesses. Notably, existing evaluations haven't specifically focused on simulated prokaryotic gene trees, which are significantly impacted by HGT.

  • Limited Empirical Validation: The scarcity of empirical studies that assess rooting methods with real-world prokaryotic data creates a significant knowledge gap. Without a clear picture of how these methods perform on actual gene families, researchers lack guidance on selecting the most reliable approach for their specific analyses.

Bridging the Knowledge Gap:

To address these limitations, the study employed a two-pronged approach:

  1. Simulated Data Analysis: The authors designed a simulation experiment to generate a large number of synthetic gene trees. These trees could be customized with varying characteristics, such as tree size, evolutionary rates, and HGT frequencies. Different rooting methods could then be evaluated on their ability to accurately identify the true root of these simulated trees.

  2. Real-World Prokaryotic Data: The study  complemented the simulations with an analysis using real gene family data from prokaryotic organisms. By carefully selecting gene families with well-understood evolutionary histories, the authors could apply different rooting methods and compare the inferred root positions with established biological knowledge.

Evaluation Criteria:

The study employed measures like Robinson-Foulds (RF) distance to compare the accuracy of different methods. The RF distance quantifies the number of topological differences between two trees. A lower RF distance between the inferred rooted tree and the true rooted tree would indicate a more accurate rooting method.

Expected Outcomes:

  • Performance Comparison: The study is expected to reveal which rooting methods perform best for prokaryotic gene trees under various evolutionary scenarios, including those with high HGT rates.

  • Factors Influencing Accuracy: The analysis of simulated and real data might identify factors that influence the accuracy of different rooting methods. These factors could include the number of gene sequences in the analysis, the evolutionary rate variation within the gene family, and the presence of specific patterns of HGT events.

The Road Ahead:

By systematically evaluating rooting methods with simulated and real prokaryotic data, this study aims to provide a valuable roadmap for researchers studying microbial gene family evolution. The insights gained from this work will empower researchers to choose the most appropriate rooting method for their specific analyses, ultimately leading to a more comprehensive understanding of the evolutionary history of genes within prokaryotic organisms. This understanding has significant implications for various fields, including microbial ecology, antibiotic resistance, and the development of novel drugs and therapeutics.

Rooting Challenges in Prokaryotic Phylogeny

The article  tackles a crucial aspect of evolutionary tree reconstruction – placing the root of the tree for gene families in prokaryotes (organisms like bacteria). This seemingly technical issue holds significance for Neo-Darwinism.

Neo-Darwinism emphasizes descent with modification through mutations and natural selection. Phylogenetic trees depict these evolutionary relationships, with the root representing the ancestral form. Accurately rooting the tree is essential for understanding the evolutionary history of genes and traits.

The challenge lies in the complex evolutionary processes in prokaryotes. These include horizontal gene transfer (HGT), where genes are exchanged between unrelated organisms. Traditional rooting methods often struggle with HGT, leading to inaccurate placements of the root.

The study by Wade et al. evaluated various rooting methods on simulated datasets mimicking prokaryotic evolution. They found that some methods, like Distance Threshold Least Squares (DTL), performed better than others, particularly with frequent gene transfer events. However, even the most accurate methods faced limitations, especially when dealing with uneven evolutionary rates across lineages. These findings highlight a challenge for Neo-Darwinian interpretations.  If the root of a gene family tree in prokaryotes cannot be confidently placed due to HGT, it becomes trickier to definitively trace the evolutionary lineage of that gene family. This can make it difficult to reconstruct the order in which traits evolved and assess the role of natural selection in shaping those traits.

The study emphasizes the need for more robust rooting methods that account for HGT and other complexities of prokaryotic evolution. Until then  exploring the history of life and the tenets of Neo-Darwinism lays incomplete.

Snippets 

Almost all standard phylogenetic methods for reconstructing gene trees result in unrooted trees; yet, many of the most useful applications of gene trees require that the gene trees be correctly rooted.

there is no information about the direction of evolution or ancestor-descendant relationships; a direct consequence of the commonly used reversible evolutionary models used for phylogeny inference.

knowledge of how a phylogeny is rooted is fundamental to understanding how genes and species evolve and almost all applications of phylogenies require phylogenetic trees to be correctly rooted.

Outgroup rooting therefore cannot be meaningfully used with gene trees that have complex histories of such evolutionary events

Even though rooting methods are widely used in practice, the accuracy of most methods has not been systematically evaluated using simulated data sets

In particular, there has never been a systematic evaluation of any of these methods on simulated prokaryotic gene trees (with horizontal gene transfer).

Furthermore, to the best of our knowledge, there is only one empirical study that uses prokaryotic data to evaluate the accuracy of some of these rooting methods

As a result, it is not known how well these methods work for rooting prokaryotic gene trees, where horizontal gene transfer is ubiquitous.

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families




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

Greatest threat to Evolution in 60 years

Image
60 years of evolution studies are threatened by nonneutral synonymous mutations. Synonymous mutations are mutations that change a codon in a gene but do not change the amino acid that is encoded by that codon. For many years, synonymous mutations were thought to be neutral, meaning that they had no effect on the fitness of an organism. However, recent research has shown that this is not always the case. In fact, many synonymous mutations can have a negative effect on fitness. This is because synonymous mutations can affect the way in which a gene is expressed. For example, a synonymous mutation can change the structure of a gene transcript, which can make it more difficult for the gene to be translated into a protein. Synonymous mutations can also affect the rate at which a gene is transcribed or translated. The discovery that synonymous mutations can be nonneutral has important implications for the study of evolution. For example, it means that we need to be more careful w
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