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Cervus. Likelihood in Cervus. Uses likelihood methods to find the most likely parents. Useful when more than one possible parent remains non-excluded.

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Cervus

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Cervus

Cervus


Likelihood in cervus

Likelihood in Cervus

  • Uses likelihood methods to find the most likely parents. Useful when more than one possible parent remains non-excluded.

  • Cervus calculates likelihood ratios, or Paternity Index (the likelihood that the candidate parent is the true parent divided by the likelihood that the candidate parent is not the true parent), and LOD scores (the log base e of the product of the likelihood ratios at each locus).

  • Delta (difference in LOD scores between the most likely parent and the second most likely parent) assesses the reliability of the assignment.

  • LOD score of 0 means that the candidate parent is equally likely as a random individual.

  • The most likely parent is the one with the most positive LOD score.


Typing errors

Typing Errors

  • Perfect data is usually not the reality.

  • A mismatch due to a typing error will exclude a true parent in a simple exclusion analysis.

  • In a likelihood analysis a single mismatch does not exclude a parent, it simply decreases the likelihood, but a true parent will probably be still identified.

  • Also good for other kinds of errors –null alleles and mutations.


Confidence level

Confidence Level

  • NOT the same as a confidence interval

  • Simulation – delta calculated for a large number of simulated parentage tests

  • Compares the distribution of deltas for tests where most likely parent was the true parent to the distribution of deltas where most likely parent was false.

  • During Parentage Analysis individual deltas are compared to simulated delta distributions

  • Critical Value of Delta (Delta criterion) – with a confidence level of 80%, value at which 4 out of 5 deltas exceeding that value came from the distribution of deltas for most likely parents that are true. 20% false positive

  • Strict and Relaxed


Input files

Input files

  • Genotype – genotypes of all individuals

  • Offspring - relationships


Pros and cons

Pros and Cons

  • Pros

    • Very user friendly

      • Excellent help file and manual

      • “Wizard” menus

      • Intuitive output file

      • Simple input files

    • Can handle minor deviations from Hardy-Weinberg equilibrium

  • Cons

    • Cannot use sex-linked loci (NewPat can…supposedly…)

    • Cannot analyze haplo-diploid or polyploid species (Kinship can)


Newpat

NewPat


Input files1

Input files

  • Needs two input files – mother/offspring and fathers

  • Files in Excel comma delimited (csv) format


Methods

Methods

  • Randomisation subroutine using “pseudo-males”


Interesting features

Interesting features

  • Sex-linked loci

    • User can define sex-linked loci

    • These loci are used if informative, but not included in relatedness calculations

  • Microtitre position

    • Checks for mistakes in gel scoring. Assumes mistakes would appear in clusters

  • Null alleles


Pros and cons1

Pros and Cons

  • Pros

    • Null alleles

    • Sex-linked loci

  • Cons

    • Horrid manual

    • Could not get the sex-linked feature to work - crashed

    • Output file confusing


Pedigree

Mom1

Dad1

Mom2

Pup1a1

Pup1a2

Pup1a3

Pup1a4

Pup2b1

Pup2b2

Pup2b3

Pup1b1

Pup1b2

Pup1b3

**

*

Pup2a1

Pup2a2

Pup2a3

Pup2a4

Pedigree

  • Not surprising that Cervus made mistakes!


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