mtDNA “Nomenclutter” and its Consequences on the Interpretation of Genetic Data

Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g., “macro-haplogroups”) vary across studies, as they depend on the sample quality, technical factors of haplogroup calling, the aims of the study, and the researchers’ understanding of the mtDNA haplogroup nomenclature. Retention of historical nomenclature coupled with a growing number of newly described mtDNA lineages results in increasingly complex and inconsistent nomenclature that does not reflect phylogeny well. This “clutter” leaves room for grouping errors and inconsistencies across scientific publications, especially when the haplogroup names are used as a proxy for secondary groupings, and represents a source for scientific misinterpretation. Here we explore the effects of phylogenetically insensitive secondary mtDNA haplogroup groupings, and the lack of standardized secondary haplogroup groupings on downstream analyses and interpretation of genetic data. We demonstrate that frequency-based analyses produce inconsistent results when different secondary mtDNA groupings are applied, and thus allow for vastly different interpretations of the same genetic data. The lack of guidelines and recommendations on how to choose appropriate secondary haplogroup groupings presents an issue for the interpretation of results, as well as their comparison and reproducibility across studies. To reduce biases originating from arbitrarily defined secondary nomenclature-based groupings, we suggest that future updates of mtDNA phylogenies aimed for the use in mtDNA haplogroup nomenclature should also provide well-defined and standardized sets of phylogenetically meaningful algorithm-based secondary haplogroup groupings such as “macro-haplogroups”, “meso-haplogroups”, and “micro-haplogroups”. Ideally, each of the secondary haplogroup grouping levels should be informative about different human population history events. Those phylogenetically informative levels of haplogroup groupings can be easily defined using TreeCluster , and then implemented into haplogroup callers such as HaploGrep3 . This would foster reproducibility across studies, provide a grouping standard for population-based studies, and reduce errors associated with haplogroup nomenclatures in future studies. ### Competing Interest Statement The authors have declared no competing interest. * NBG : Nomenclature-Based Groupings SC : Single Character grouping SCL : Single Character and L with one digit grouping ABG : Algorithm-Based Groupings mtDNA : Mitochondrial DNA rCRS : The revised Cambridge Reference Sequence RSRS : The Reconstructed Sapiens Reference Sequence MDS : Multidimensional scaling CA : Correspondence analysis rhb_01 : Results of rhierBAPS level 1 rhb_02 : Results of rhierBAPS level 2 rhb_03 : Results of rhierBAPS level 3 tc_0.006 : Results of TreeCluster with the threshold value of 0.006 tc_0.005 : Results of TreeCluster with the threshold value of 0.005 tc_0.004 : Results of TreeCluster with the threshold value of 0.004 tc_0.003 : Results of TreeCluster with the threshold value of 0.003 * ACB : African Caribbean in Barbados ASW : African Ancestry in SW USA MSL : Mende in Sierra Leone GWD : Gambian in Western Division – Mandinka ESN : Esan in Nigeria YRI : Yoruba in Ibadan, Nigeria LWK : Luhya in Webuye, Kenya