Related Experiment Video
Updated: Jun 3, 2026
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework
Jean-Philippe Doyon1, Sylvie Hamel, Cedric Chauve
1LIRMM, Montpellier.
Summary
Inferring gene family evolution requires gene tree/species tree reconciliation. A new probabilistic method efficiently computes reconciliation probabilities, aiding evolutionary genomics research.
Area of Science:
- Evolutionary genomics
- Functional genomics
Background:
- Inferring gene family evolutionary scenarios is crucial for functional and evolutionary genomics.
- Gene tree/species tree reconciliation is a common approach, often using discrete parsimony to minimize gene duplications/losses.
- Probabilistic methods, like the birth-and-death process, offer advanced tools for reconciliation and orthology prediction.
Purpose of the Study:
- To adapt an existing algorithm for efficient computation of posterior probabilities of gene tree/species tree reconciliations.
- To analyze the probabilistic landscape of reconciliations using real fungal gene family data and synthetic datasets.
Main Methods:
- Algorithm for exploring the entire space of gene tree/species tree reconciliations.
- Computation of exact or approximated posterior probabilities of reconciliations.
- Analysis of fungal gene families and synthetic gene trees.
Main Results:
- The adapted algorithm efficiently computes posterior probabilities of reconciliations.
- Analysis of real and synthetic datasets reveals insights into the probabilistic landscape of reconciliations.
- Simulations show that a small subset of reconciliations is often sufficient for accurate probability approximation.
Conclusions:
- For gene trees from simple birth-and-death processes with realistic rates, exploring a small subset of reconciliations closely approximates the most likely reconciliation probabilities.
- The method efficiently explores relevant subspaces of reconciliations when probabilities are more evenly distributed.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
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...
01:28Microbial Phylogeny
Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
02:05Gene Evolution - Fast or Slow?
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.
In contrast, regions which code...
In contrast, regions which code...
02:05Gene Evolution - Fast or Slow?
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.
In contrast, regions which code...
In contrast, regions which code...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
02:16Genetics of Speciation
Speciation is the evolutionary process resulting in the formation of new, distinct species—groups of reproductively isolated populations.The genetics of speciation involves the different traits or isolating mechanisms preventing gene exchange, leading to reproductive isolation. Reproductive isolation can be due to reproductive barriers that have effects either before or after the formation of a zygote. Pre-zygotic mechanisms prevent fertilization from occurring, and post-zygotic mechanisms...