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Related Concept Videos

Limits to Natural Selection01:38

Limits to Natural Selection

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Organisms that are well-adapted to their environment are more likely to survive and reproduce. However, natural selection does not lead to perfectly adapted organisms. Several factors constrain natural selection.
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What is Natural Selection?01:32

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Natural selection is an evolutionary process in which individuals with survival-promoting traits reproduce at higher rates. These favorable traits become more common within a population or species. Naturally selected traits initially arise via random genetic mutations. In order for selection to occur, there must be variation within a population, the trait controlling the variation must be heritable, and there must be an evolutionary advantage for variation in the trait.
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Types of Selection01:46

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Natural selection influences the frequencies of particular alleles and phenotypes within populations in several different ways. Primarily, natural selection can be directional, stabilizing, or disruptive. Directional selection favors one extreme trait and shifts the population towards that phenotype while selecting against individuals displaying alternate traits. Stabilizing selection favors an intermediate trait with a narrow range of variation. Deviation from the optimal phenotype towards an...
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Natural Selection and Mating Preferences01:06

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The principle of natural selection posits that organisms better adapted to their environment are more likely to survive and reproduce. This principle is closely intertwined with mating preferences, a key aspect of sexual selection, which evolutionary psychologists believe is driven by instincts to propagate one's genes. Such instincts significantly influence mating behaviors and preferences between genders.
Females, due to their biological roles in conception, pregnancy, and nursing,...
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Genetic Drift03:33

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Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.
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Frequency-dependent Selection01:21

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When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.
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Measuring Natural Selection.

Anders Gonçalves da Silva1

  • 1Microbiological Diagnostic Unit (MDU), Public Health Laboratory, Doherty Institute, 792 Elizabeth St., Melbourne, VIC, 3000, Australia. andersgs@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|November 30, 2016
PubMed
Summary

This chapter explains the core algorithm of the CODEML model within the PAML software package. Understanding this computational evolutionary biology model helps researchers design their own analyses.

Keywords:
Branch modelsBranch-Site modelsCODEMLCodon substitution modelNatural selectionPAMLSite modelsdN/dS ratio

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Area of Science:

  • Computational evolutionary biology
  • Bioinformatics software

Background:

  • The CODEML model is a key component of the PAML software package.
  • Existing literature and manuals provide extensive details on CODEML.

Purpose of the Study:

  • To provide a foundational understanding of the CODEML algorithm.
  • To serve as a companion guide to the PAML software manual.
  • To empower researchers to design their own evolutionary analyses using CODEML.

Main Methods:

  • Review of the fundamental algorithm underpinning the CODEML model.
  • Explanation of its implementation within the PAML software.

Main Results:

  • A clear explanation of the CODEML model's operational principles.
  • Sufficient detail to enable users to plan custom analyses.

Conclusions:

  • Researchers will gain a working knowledge of the CODEML algorithm.
  • The chapter facilitates independent design and execution of evolutionary studies using CODEML.