Parentage Analysis

Parental Reconstruction

GERUD1.0: This program is the original parental reconstruction program from Jones (2001). Download GERUD1.0 from GitHub.

Reference: Jones AG (2001) GERUD1.0: A computer program for the reconstruction of parental genotypes from progeny arrays using multilocus DNA data. Molecular Ecology Notes 1:215-218.

GERUD2.0: Version 2.0 extends and improves GERUD1.0. In general, GERUD2.0 should be used for most purposes. It’s available on GitHub.

Reference: Jones AG (2005) GERUD2.0: A computer program for the reconstruction of parental genotypes from half-sib progeny arrays with known or unknown parents. Molecular Ecology Notes 5:708-711.

GERUD3.0: Version 3.0 of GERUD is a command-line version, which can run on Windows or any other operating system with a C++ compiler. The command-line interface makes this version suitable for use on supercomputers. Otherwise the functionality is very similar to that of GERUD2. If you use GERUD3, please cite the above papers for now (until we have time to publish a program note). GERUD3 and GERUDsim3 are available on the new JonesLabIdaho GitHub page.

Estimating Mating System Variable based on Bateman’s Principles

If you’re interested in the opportunity for sexual selection or the Bateman gradient, and you have data on mating and reproductive success for a set of individuals (male or female), you can use Batemanater to estimate these variables. It also bootstraps for confidence intervals. You first need to read these two papers to decide if your data set is likely to suffer from substantial bias:

Mobley KB and Jones AG (2013) Overcoming statistical bias to estimate genetic mating system parameters in open populations: A comparison of Bateman’s principles between the sexes in a sex-role-reversed pipefish. Evolution 67:646-660.

Jones AG (2015) BATEMANATER: A computer program to estimate and bootstrap mating system variables based on Bateman’s principles. Molecular Ecology Resources 15:1396-1402.

Whether or not your data set suffers from bias, you can still use BATEMANATER to estimate the mating system variables of interest. You can get the program on GitHub.