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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...
Phylogenetic Trees03:21

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

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...
Microbial Phylogeny01:28

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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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Genetics 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...
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Speciation Rates

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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Related Experiment Video

Updated: Jun 25, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

Laura S Kubatko1, Bryan C Carstens, L Lacey Knowles

  • 1Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA. lkubatko@stat.osu.edu

Bioinformatics (Oxford, England)
|February 13, 2009
PubMed
Summary
This summary is machine-generated.

STEM is a C language software package for phylogenetic species tree estimation using maximum likelihood (ML) under the coalescent model. It efficiently computes ML species trees and branch lengths, aiding evolutionary studies.

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Genetics

Background:

  • Phylogenetic species tree estimation is crucial for understanding evolutionary relationships.
  • The coalescent model provides a framework for inferring species trees from gene trees.
  • Accurate estimation of species trees requires robust computational tools.

Purpose of the Study:

  • To introduce STEM, a software package for maximum likelihood (ML) estimation of phylogenetic species trees.
  • To provide tools for computing ML species trees from gene trees under the coalescent model.
  • To enable efficient searching for top-likelihood species trees and ML branch length computation.

Main Methods:

  • The STEM software package is implemented in the C programming language.
  • It utilizes the coalescent model to infer species trees from gene tree data.
  • Maximum likelihood estimation is employed for tree and branch length calculations.

Main Results:

  • STEM provides options to compute the ML species tree.
  • The software can search the space of all species trees to identify the k trees with the highest likelihood.
  • ML branch lengths can be computed for user-provided species trees.

Conclusions:

  • STEM offers a comprehensive solution for phylogenetic species tree inference.
  • The package facilitates robust estimation of evolutionary relationships using ML and the coalescent model.
  • Availability of source code promotes wider adoption and further development in computational phylogenetics.