Locus and Non-Locus Specific Technical Caveats: An Overview of Their Occurrence in Tilapiine Cichlids Genetic Data and Approaches to Salvage Loci

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Abstract
Many tilapia-related research papers make assumptions in relation to Locus- and Non-Locus-Specific Technical Problems (LTPs) that hinder the reaching of clear genetic monitoring conclusions. Since LTPs have implications for decisions related to fisheries and aquaculture management, an overview of the key LTPs affecting tilapia population studies will help geneticists not only to consider them, but also to know the gaps that exist in order to guide future research within the domain. Using a meta-analysis, we present approaches to distinguish the LTPs from each other, which is most often needed for tilapia genetic data before any statistical inference is made. Each LTP and the approaches to make the genetic data reliable are presented and discussed. Cultured tilapia populations are generally characterized by homogamy, heterogamy, heterosis, inbreeding and overdominance. In contrast, null alleles, allelic dropout, stuttering, homoplasy, genetic bottleneck and Wahlund effect are most often at issue in populations originating only from the wild. Future perspectives are needed about the components underlying the LTPs related to genotyping errors and biological factors.