Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea)

Abstract

The Coccinellidae are one of the most familiar beetle families, the ladybirds. Despite the great ecological and economic significance, the phylogenetic relationships of Coccinellidae remain poorly understood. One of the reasons is that the sequenced mitogenomes available for this family are very limited. We sequenced complete or nearly complete mitogenomes from seven species of the tribe Coccinellini with next-generation sequencing. All species have the same gene content and gene order as the putatively ancestral insect mitogenome. A large intergenic spacer region (> 890 bp) was found located between trnI and trnQ. The potential for using secondary structures of the large and small ribosomal subunits for phylogenetic reconstruction was predicted. The phylogenetic relationships were explored through comparative analyses across more than 30 coccinellid species. We performed phylogenetic analyses with both concatenation methods (Maximum Likelihood and Bayesian Inference) and multispecies coalescent method (ASTRAL). Phylogenetic results strongly supported the monophyly of Coccinellidae. Within Coccinellidae, the Epilachnini and the Coccinellini including Halyziini were monophyletic, while the Scymnini and Coccidulini were non-monophyletic.

A New Species of Scymnus (Coleoptera, Coccinellidae) from Pakistan with Mitochondrial Genome and Its Phylogenetic Implications

“…The tribes Chilocorini, Epilachnini, Hyperaspini, Scymnini, and Coccidulini are often considered paraphyletic or polyphyletic [57,82]. Our mitochondrial genome data supported a sister-group relationship between Coccidulini and the clade Epilachnini (Epivertini + Subcoccinellini), consistent with the mitochondrial sequence findings of Zhang et al [65].…”

“…Che et al [13] conducted a comprehensive study on the phylogenetic relationships within the family Coccinellidae, providing strong support for the notion of the monophyly of several tribes within the subfamily Coccinellinae. Their research consistently found Coccinellini to be monophyletic, which contrasts with previous studies [11,55,57,76,81,82] that have suggested it to be the sister group of Chilocorini. Our results also recovered a similar branching pattern showing Coccinellini as a sister to Chilocorini based on the mitogenome data (Figure 6).…”

Phylogenetic Implication of Large Intergenic Spacers: Insights from a Mitogenomic Comparison of Prosopocoilus Stag Beetles (Coleoptera: Lucanidae)

“…The IGSs have also been found between different genes in the mitogenomes of other beetles, such as between trnW and trnC [8], nad2, and trnW [21], trnI and trnQ [4,22,23], and so on. Comparative analyses of IGSs suggest that the presence and location of the IGS may be useful for studying evolutionary history and species delimitation in insects [24,25], such as those in the families Meloidae [8,13], Cleridae [16], and Scarabaeoidae [18]. Although a recent study reported that the Dorcus velutinus complex had a large IGS (>50 bp) between trnS2 (UCN) and nad1 [20], very little is known about large IGSs in Prosopocoilus mitogenomes.…”

Contribution to the Knowledge of Dicranoptychini (Diptera, Tipuloidea, Limoniidae) in China, with the First Mitochondrial Genome of the Tribe and Its Phylogenetic Implications

“…The descriptions and illustrations of the males and females, as well as the first key to Chinese Dicranoptycha crane flies based on the type and non-type specimens and literature, are presented. Due to maternal inheritance, rapid evolution, and highly conserved gene content, the mitochondrial (mt) genome has been widely used in insect phylogenetic research [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 ]. In 2016, we reported the first three mt genomes of Limoniidae [ 5 ].…”