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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Phylogenetic Trees03:21

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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Phylogeny01:23

Phylogeny

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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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Gene Evolution - Fast or Slow?02:05

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Related Experiment Video

Updated: Jun 17, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Differentiable phylogenetics via hyperbolic embeddings with Dodonaphy.

Matthew Macaulay1, Mathieu Fourment1

  • 1Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia.

Bioinformatics Advances
|August 12, 2024
PubMed
Summary

We introduce soft-NJ, a differentiable method for phylogenetic tree optimization. This approach enables gradient-based methods in hyperbolic spaces for efficient phylogenetic inference, advancing computational phylogenetics.

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Area of Science:

  • Computational Phylogenetics
  • Machine Learning
  • Bioinformatics

Background:

  • Optimizing phylogenetic trees in high-dimensional discrete spaces is computationally challenging.
  • Hyperbolic embeddings offer efficient continuous space encoding for trees.
  • Differentiable tree decoders are necessary for optimizing phylogenetic likelihoods.

Purpose of the Study:

  • To present soft-NJ, a differentiable version of the Neighbor-Joining algorithm.
  • To enable gradient-based optimization directly over the space of phylogenetic trees.
  • To apply differentiable tree embeddings for variational Bayesian phylogenetics.

Main Methods:

  • Developed soft-NJ, a differentiable tree decoder for phylogenetic analysis.
  • Utilized hyperbolic embeddings for efficient tree representation in continuous space.
  • Performed variational Bayesian inference by optimizing embedding distributions.

Main Results:

  • Demonstrated the potential of differentiable optimization for maximum likelihood inference.
  • Evaluated soft-NJ's performance on eight benchmark datasets against state-of-the-art methods.
  • Showcased soft-NJ as a powerful and efficient approach for phylogenetics via tree embeddings, despite potential local optima.

Conclusions:

  • Soft-NJ facilitates gradient-based optimization in the space of phylogenetic trees.
  • Hyperbolic embeddings combined with soft-NJ offer a parametrically efficient approach to phylogenetics.
  • The Dodonaphy software package implements soft-NJ, making it accessible for research.