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sofsog : a suite of programs to avoid inbreeding in plantation designs
Author(s) -
FERNÁNDEZ J.,
GONZÁLEZMARTÍNEZ S. C.
Publication year - 2010
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/j.1755-0998.2009.02764.x
Subject(s) - biology , inbreeding , neighbourhood (mathematics) , weighting , limiting , suite , ecology , statistics , demography , population , mathematics , medicine , mechanical engineering , mathematical analysis , history , archaeology , sociology , engineering , radiology
Cost‐effective ways of controlling inbreeding in conservation or productive plantations imply the allocation of individuals reducing the possibility of close relatives’ mating and, consequently, limiting inbreeding. sofsog is a suite of programs, which helps to design plantation sites. First, if the plantation scheme involves several plots, it allows distribution of individuals available among different sites minimizing within‐site global coancestry. Then, it yields a plantation design for each site, either following the classical permutated neighbourhood strategy or the recently developed method by Fernández and González‐Martínez. This new method allows the implementation of different pollen dispersion kernels, and to include in the designing strategy any available information on individual relationships, reproductive success, differences in phenology, etc., via weighting or penalization matrices. Additionally, the package includes a tool for calculating the molecular coancestry (Identity By State) from codominant marker data.