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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I,...
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In most organisms, sex is determined by the ratio of X and Y chromosomes. However, in some organisms, such as Drosophila and C.elegans, sex is determined by the ratio of the number of X chromosomes to the number of sets of autosomes. The Y chromosome in Drosophila is active but does not determine sex. It contains genes responsible for the production of sperms in adult flies.  
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In animals, gender is determined by the number and type of sex chromosome. For example, human females have two X chromosomes, and males have one X and one Y chromosome, whereas C.elegans with one X chromosome is a male, and the one with two X chromosomes is a hermaphrodite.
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Related Experiment Video

Updated: Jan 11, 2026

Identification of Homologous Recombination Events in Mouse Embryonic Stem Cells Using Southern Blotting and Polymerase Chain Reaction
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Sex-specific evolutionary programs shape recombination rate evolution in house mice.

Lydia K Wooldridge1, Micah Pietraho1, Peyton DiSiena1

  • 1The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, United States.

Genetics
|November 14, 2025
PubMed
Summary
This summary is machine-generated.

Male recombination rates in house mice (Mus musculus) show strong evolutionary signals linked to phylogeny, unlike females. Evidence suggests an adaptive increase in male recombination in the M. m. musculus subspecies lineage.

Keywords:
genetic conflicthouse micephylogenetic comparative methodsrecombination ratesex dimorphism

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Preparation of Meiotic Chromosome Spreads from Mouse Oocytes for Assessment of Synapsis and Recombination
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Area of Science:

  • Evolutionary biology
  • Genetics
  • Comparative genomics

Background:

  • Recombination rates exhibit significant variation across species, populations, and sexes.
  • House mice (Mus musculus) display extreme differences in recombination rates, with males showing greater variation than females.
  • Sex-limited variation suggests distinct evolutionary mechanisms for male and female recombination rates in M. musculus.

Purpose of the Study:

  • To formally evaluate the hypothesis of distinct evolutionary mechanisms for male and female recombination rates in Mus musculus using a phylogenetic framework.
  • To investigate the phylogenetic distribution and evolutionary history of sex-specific recombination rates across Mus species and M. musculus subspecies.

Main Methods:

  • Compiled a large dataset of sex-specific crossover rate estimates from over 6,000 meiotic cells.
  • Included data from 31 genetically diverse inbred mouse strains across five Mus species and four M. musculus subspecies.
  • Combined cytogenetic estimates with published data for phylogenetic analysis.

Main Results:

  • Male recombination rates showed a strong phylogenetic signal (HP2 = 0.82), well predicted by the Mus phylogeny.
  • Female recombination rates exhibited a weaker phylogenetic signal (HP2 = 0.24).
  • M. m. musculus males displayed a marked increase in recombination rate compared to other M. musculus subspecies males, with evidence for adaptive lineage-specific evolution.

Conclusions:

  • Recombination rate evolution in house mice is governed by distinct sex-specific evolutionary regimes.
  • Findings support the hypothesis of separate evolutionary pathways for male and female recombination rates.
  • Motivates future research into sex-specific selective pressures and genetic architectures influencing recombination.