info:eu-repo/semantics/review In this research, we focused on the following question: What element can be used for phylogeography and phylogenetic studies for all species using results of the genome-wide analysis (GWA) of numerous model organisms (e.g., Homo sapiens, Mus musculus, Drosophila melanogaster)? We especially paid attention to the average mutation rate variation in the DNA fragment size across alleles from diverse loci (i.e., related to length-dependent mutation processes). Over the past 30 years, all molecular markers have been developed from the fundamentally different mechanisms of four mutations: single-nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), insertions–deletions (INDELs), and chromosome aberrations. The challenge is to accurately fix the molecular clock for size-variant DNA marker data to uncover the phylogeographic histories of many plants and animals. In this paper, we provided a lot of examples from a Homo sapience to a forest tree from Pinus genus, illustrating the importance of differentiating between molecular markers, their origins, and the locus molecular size to better calibrate the molecular clock for back-in-time simulation analyses Naydenov, Krassimir D. Naydenov, Michel K. Alexandrov, Alexander Gurov, Todor Hinkov, Georgi Ivanovska, Sofiya Gyuleva, Veselka Gurova, Silvi-Maria Balakumar, Makech Nikolić, Biljana genome analysis, length-dependent mutation processes, molecular clock, phylogeography http://creativecommons.org/licenses/by/4.0/legalcode University of Forestry, Sofia eng https://unilib.phaidrabg.rs/o:6158 cobiss:1238932196 ISSN: 1314-3905 application/pdf 735353 bytes Molecular markers vs. phylogeographic memory dilemma: an example of length-dependent mutation processes 2024 Forestry ideas volume: 30 startpage: 272 endpage: 287