Abstract
Anonymous non-coding sequence markers (ANMs) are powerful neutral genetic markers with great utility in phylogeography, population genetics and population genomics. Developing ANMs has previously relied on sequencing random fragments of genomic DNA in the target species and then querying bioinformatics databases to identify unannotated, putatively neutral fragments. Here, we describe an alternative in silico approach that is based on identifying large unannotated genomic regions in model species to provide a priori neutral targets for candidate ANMs that are remote from exonic regions. We illustrate this approach by developing a set of 17 polymorphic ANMs for red grouse (Lagopus lagopus scotica) from c. 1 Mbp non-coding chromosome regions of chicken, turkey and zebrafinch genomes. This pipeline presents a powerful and efficient approach when appropriate model genomes are available for the target species of interest.
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