Open AccessRecent insertion/deletion (re INDEL ) mutations: increasing awareness to boost molecular‐based research in ecology and evolution
Author(s) -
SchlickSteiner Birgit C.,
Arthofer Wolfgang,
Moder Karl,
Steiner Florian M.
Publication year - 2015
Publication title -
ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.17
H-Index - 63
ISSN - 2045-7758
DOI - 10.1002/ece3.1330
Subject(s) - indel , biology , computational biology , indel mutation , identification (biology) , dna sequencing , evolutionary biology , genetics , molecular evolution , mutation , dna , phylogenetic tree , gene , ecology , single nucleotide polymorphism , genotype
Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion ( INDEL ) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDEL s would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (re INDEL ) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for re INDEL identification is knowledge about the pedigree of the individuals sampled. Sound re INDEL knowledge will allow the improved modeling needed for including INDEL s in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next‐generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for re INDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few re INDEL s identified. As most likely explanation, we hypothesize that re INDEL s are underreported rather than absent and that this underreporting stems from common re INDEL unawareness. If our hypothesis applies, increased re INDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of re INDEL s together with standardized key information on the nature of mutations when they are detected and the use of the keyword “re INDEL ” to increase visibility in both instances of successful and unsuccessful search.