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Related Concept Videos

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.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
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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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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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Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
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Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
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Related Experiment Video

Updated: Mar 5, 2026

Identification of Homologous Recombination Events in Mouse Embryonic Stem Cells Using Southern Blotting and Polymerase Chain Reaction
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Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach.

Brice A J Sarver1, Sara Keeble1, Ted Cosart1

  • 1Division of Biological Sciences, University of Montana, Missoula, MT.

Genome Biology and Evolution
|March 25, 2017
PubMed
Summary
This summary is machine-generated.

We developed a pseudoreference method to improve genomic data analysis across species. This approach reduces mapping bias and enhances evolutionary studies, particularly for the Mus genus.

Keywords:
Mus musculusbioinformaticscomparative genomicsintrogressionmapping bias

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Related Experiment Videos

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Comparative genomics relies heavily on high-quality reference genomes.
  • Limited genomic resources for specific species necessitate using divergent references, introducing bias.
  • Existing analytical frameworks struggle with interspecies genomic comparisons.

Purpose of the Study:

  • To develop a scalable pseudoreference approach for incorporating sample-specific variation into genome references.
  • To reduce systematic mapping bias in downstream genomic analyses.
  • To improve evolutionary and phylogenomic studies across diverse taxa.

Main Methods:

  • Developed a scalable pseudoreference approach to iteratively incorporate sample-specific variation.
  • Used targeted capture to sequence whole exomes (54 Mbp) in 12 mouse lineages (ten species).
  • Generated whole exome pseudoreferences for all species within the Mus radiation.

Main Results:

  • The pseudoreference approach improved basic genomic analyses dependent on mapping accuracy.
  • Preserved existing annotations from the mouse reference genome.
  • Successfully resolved evolutionary relationships among mouse lineages, accounting for phylogenetic discordance.
  • Identified patterns of genomic introgression among lineages.

Conclusions:

  • The pseudoreference framework enhances comparative genomic analyses by reducing mapping bias.
  • This method provides a valuable resource for phylogenomic studies in mice and is adaptable to other systems.
  • Facilitates more accurate evolutionary relationship resolution and introgression pattern analysis.