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Related Concept Videos

Phylogenetic Trees03:21

Phylogenetic Trees

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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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Evolutionary Relationships through Genome Comparisons02:54

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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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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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Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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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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Synteny and Evolution02:31

Synteny and Evolution

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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The limits of phylogenetic analysis: identifying analytical hallucinations.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Phylogenetic supergraphs.

Ward C Wheeler1

  • 1Division of Invertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY, 10024, USA.

Cladistics : the International Journal of the Willi Hennig Society
|January 20, 2022
PubMed
Summary
This summary is machine-generated.

Phylogenetic analysis now uses general directed acyclic graphs beyond trees. New supergraph methods reconcile multiple graphs, serving as summaries or starting points for further research.

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Area of Science:

  • Evolutionary biology
  • Computational phylogenetics
  • Bioinformatics

Background:

  • Phylogenetic analyses traditionally relied on tree structures.
  • Empirical and theoretical studies increasingly utilize more complex graph structures like directed acyclic graphs (DAGs), networks, and forests.
  • Existing consensus and supertree techniques are limited in handling these generalized graph structures.

Purpose of the Study:

  • To extend existing consensus and supertree techniques to a broader class of phylogenetic graphs.
  • To introduce a set of phylogenetic supergraph methods capable of reconciling multiple DAGs, networks, and forests.
  • To provide methods for summarizing complex phylogenetic results or generating heuristic starting points for further analysis.

Main Methods:

  • Development of novel algorithms for reconciling multiple directed acyclic graphs.
  • Adaptation and extension of established consensus and supertree methodologies.
  • Implementation of phylogenetic supergraph techniques.

Main Results:

  • A novel set of phylogenetic supergraph methods is presented.
  • These methods effectively reconcile multiple general directed acyclic graphs, including networks and forests.
  • The developed supergraph techniques offer a means to synthesize diverse phylogenetic data.

Conclusions:

  • The proposed phylogenetic supergraph methods advance the field by accommodating complex graph structures beyond traditional trees.
  • These methods provide valuable tools for summarizing and initiating phylogenetic analyses involving networks and forests.
  • The work facilitates more comprehensive and nuanced evolutionary reconstructions.