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Related Concept Videos

Hybrid Zones02:29

Hybrid Zones

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Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may possess distinct phenotypic or genetic differences that impact their survival and reproductive success. The genetic variances introduced by hybridization influence species diversity and speciation processes within the hybrid zone.
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Some of Mendel’s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A trihybrid cross is a combination of three individual monohybrid crosses. For example, plant height (tall vs. short), seed shape (round vs. wrinkled), and seed color (yellow vs. green).
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Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
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Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization

Leo Zeitler1, Kimberly J Gilbert1

  • 1Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland.

Genome Biology and Evolution
|June 27, 2024
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Summary

Runs of homozygosity (ROHs) reveal inbreeding. This study shows that ROH patterns can distinguish self-fertilization from other inbreeding causes, even with complex population histories.

Keywords:
demographic historyinbreedingmating systemoutcrossing raterandom forestruns of homozygosityself-fertilization

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Area of Science:

  • Population Genetics
  • Genomics
  • Evolutionary Biology

Background:

  • Runs of homozygosity (ROHs) indicate inbreeding and are used in conservation and breeding.
  • Self-fertilization increases homozygosity and generates long ROHs, but its impact on ROH characteristics and potential confounding with demographic effects is unclear.

Purpose of the Study:

  • To investigate how reproductive mode (selfing vs. outcrossing) and demographic history influence ROH patterns.
  • To develop methods for distinguishing self-fertilization from other inbreeding sources using ROHs.
  • To predict selfing rates and demographic histories from genomic data.

Main Methods:

  • Simulations were used to model the effects of reproduction mode and population demography on ROHs.
  • Random forest models were applied to identify unique ROH features indicative of different inbreeding types.
  • The models were validated using additional simulations and empirical data from selfing and mixed-mating species.

Main Results:

  • Distinct ROH features were identified that differentiate self-fertilization from other inbreeding sources.
  • Selfing rates were accurately predicted even in the presence of complex demographic histories.
  • Population genetic summary statistics enhanced model accuracy, especially with additional inbreeding events like bottlenecks.

Conclusions:

  • ROHs are valuable for disentangling various sources of inbreeding, although some confounding may persist.
  • The developed random forest models offer a novel tool for inferring selfing rates from genomic data.
  • This approach aids in understanding population structure, mating systems, and evolutionary trajectories.