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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary 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...
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Phylogenetic Trees

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Microbial Phylogeny01:28

Microbial 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,...
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Phylogeny

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...
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Speciation can proceed at markedly different rates, and evolutionary biologists commonly describe these differences through the models of gradualism and punctuated equilibrium. Both patterns explain how new species arise, but they differ in the tempo and continuity of evolutionary change. In both cases, evolutionary change arises from heritable variation within populations, with natural selection often shaping traits that improve survival and reproduction under specific environmental conditions.

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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Coalescent methods for estimating phylogenetic trees.

Liang Liu1, Lili Yu, Laura Kubatko

  • 1Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford street, Cambridge, MA 02138, USA.

Molecular Phylogenetics and Evolution
|June 9, 2009
PubMed
Summary
This summary is machine-generated.

This review covers new models for estimating species phylogenetic trees using the multispecies coalescent model. These methods address gene tree heterogeneity and offer a more accurate view of evolutionary relationships than traditional approaches.

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Area of Science:

  • Phylogenetics
  • Evolutionary Biology
  • Computational Biology

Background:

  • The distinction between gene trees and species trees is crucial in phylogenetics.
  • Gene tree heterogeneity can arise from factors like deep coalescence.
  • Explicit species tree estimation methods are a recent development.

Purpose of the Study:

  • To review recent models for estimating phylogenetic trees under the multispecies coalescent.
  • To highlight the importance of explicit species tree estimation.
  • To discuss the challenges and future directions in species tree inference.

Main Methods:

  • Bayesian approaches utilizing nucleotide substitution and gene tree probability distributions.
  • Parametric and nonparametric methods including parsimony, summary statistics, supertree, and consensus methods.
  • Modeling deep coalescence due to random genetic drift.

Main Results:

  • Explicit species tree methods can outperform concatenation when gene trees are misleading.
  • Sampling many independent loci is crucial for accurate species tree estimation.
  • Current models are being refined to incorporate factors like gene flow and molecular clock deviations.

Conclusions:

  • Species tree approaches are a valuable goal for systematics.
  • Advanced coalescent models are necessary to capture complex evolutionary forces.
  • Further research is needed to refine models and computational efficiency.