Highlighting the classification of mitochondrial DNA haplogroups C and D in chickens.

Mitochondrial DNA (mtDNA) has been widely used in tracing the matrilineal history of domestic chickens based on haplogroup trees generated by parsimony-like method (Lan et al. 2017). However, the increasing amount of data using different nomenclature for mtDNA phylogeny complicates comparisons across studies (Miao et al. 2013; Peng et al. 2015; LuzuriagaNeira et al. 2017; Huang et al. 2018; Al-Jumaili et al. 2020; Quan et al. 2020). A standardized, hierarchical haplogroup nomenclature system can benefit studies that involve matrilineal evolutionary genetics (Wang et al. 2014; Peng et al. 2015; Schr€ oder et al. 2016; Adeola et al. 2017; Wang et al. 2019; Zhang et al. 2020). Thus, a better understanding of chicken matrilineal genealogy urgently requires such a coherent nomenclature system. The common A–I nomenclature was first produced by Liu et al. (2006), using a phylogenetic framework to identify lineages based on a large D-loop dataset. However, because the D-loop has a high mutation rate and recurrent mutations, the structure of the matrilineal genealogy is often blurred. In response, a hierarchical haplogroup tree with the higher resolution was later constructed based on both D-loop sequences and mtDNA genomes (mtgenomes) (Miao et al. 2013). This updated tree retained the original nomenclature for haplogroups A–G, but defined several new haplogroups (H, I, and W–Z), sub-haplogroups (e.g. C1, C2, and C3), and macro-haplogroups (ABZY, CD, and EFGHIWX). Additionally, the nomenclature was altered if discordant between the D-loop and mtgenome. For instance, some sequences previously in clade C based on D-loop data became haplogroup X using mtgenome data, while other sequences originally in clade D were moved to haplogroups Y and C. Several clades of red junglefowl from Thailand were previously classified into haplogroup C based on D-loop information (Miao et al. 2013), were re-clustered as new haplogroup V at the basal branch of haplogroup CD (Huang et al. 2018). The classification of haplogroup C and D in chickens often changes depending on phylogeny construction methods, resulting in controversy. For example, recent definitions of these two groups (Quan et al. 2020) conflicted with those in the previous studies (Miao et al. 2013; Huang et al. 2018). Our reanalysis categorized only 33 sequences to sub-haplogroup C1, versus 236 sequences in Quan et al. (2020), and we also found that haplogroup C frequency in Southwest China was only 2.37% (Table S1). In another study, sub-haplogroup C2 in the nomenclature of Miao et al. (2013) was classified into haplogroup D (Table S2) (Al-Jumaili et al. 2020). This change may generate confusion for future studies because haplogroups C and D are increasingly used as potential candidate markers for exploring chicken origins and expansion, particularly in northern China and the Pacific (Miao et al. 2013; Xiang et al. 2014; Dyomin et al. 2017; Herrera et al. 2017; Zhang et al. 2017; Ulfah et al. 2017; Huang et al. 2018; Al-Jumaili et al. 2020). Therefore, the classification of the two haplogroups must be clarified as quickly and as accurately as possible. An alternative