Mitogenome evolution in ladybirds: Potential association with dietary adaptation

Abstract

Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein-coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits. K E Y W O R D S diet evolution, mitochondrial DNA, molecular phylogeny, negative selection, positive selection | 1043 YUAN et Al.

New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses

“…The predicted secondary structure and anticodon sequence for 21 tRNAs of the E. patagonia mitogenome is similar that reported to other ladybird beetles [65,71]. As was also noted by [65], the most variations are in substitutions, and indels (insertion, deletion of bases) of the tRNA among the Coccinellidae are present in the variable and D loops, and TψC arm, which is reflected in the differences in the size of this arm and its D-loop.…”

“…The predicted secondary structure and anticodon sequence for 21 tRNAs of the E. patagonia mitogenome is similar that reported to other ladybird beetles [65,71]. As was also noted by [65], the most variations are in substitutions, and indels (insertion, deletion of bases) of the tRNA among the Coccinellidae are present in the variable and D loops, and TψC arm, which is reflected in the differences in the size of this arm and its D-loop. Eriopis patagonia share with Aiolocaria hexaspilota, Calvia muiri (Timberlake), C. septempunctata, Illeis cincta Fabricius, and Propylea japonica a lack of the TψC arm in tRNA-Pro, which is replaced by the loop [71], while in other species, the TψC arm is present in this tRNA [65].…”

“…Coccinellinae is also divided into two main clades (clade Coccinellini and the other clade including Coccidulini, Epilachnini, Scymnini) with high support (PCG_RNA and PCG12_RNA: FB and TBE = 100; PP = 1.0/PCG_AA: FB = 67; PP = 0.84). The generic composition between the main clades and inside each clade of Coccinellini (here A-F) differs slightly to the previous studies of Escalona et al [83], which includes one mitochondrial and four nuclear markers that Song et al [71] and Yuan et al [65] based on complete mitochondrial genomes. Regarding the main clades within Coccinellini, here, this tribe is divided into two principal clades (A and B, the latter including clades C and D), as also recovered by Song et al ([71]; Figures 3 and 4).…”

“…It is the first published and characterized mitogenome for this genus obtained from an old specimen from a Natural History Collection. The order and orientation of the genes in the mitogenome of E. patagonia are consistent with those of other mitochondrial genomes of Coccinellidae [42,[62][63][64][65][66][67][68][69][70][71][72][73] and contain the typical set of mitochondrial genes found in insects.…”

“…As was also noted by [65], the most variations are in substitutions, and indels (insertion, deletion of bases) of the tRNA among the Coccinellidae are present in the variable and D loops, and TψC arm, which is reflected in the differences in the size of this arm and its D-loop. Eriopis patagonia share with Aiolocaria hexaspilota, Calvia muiri (Timberlake), C. septempunctata, Illeis cincta Fabricius, and Propylea japonica a lack of the TψC arm in tRNA-Pro, which is replaced by the loop [71], while in other species, the TψC arm is present in this tRNA [65]. The Eriopis patagonia mitogenome has the smallest D-loop in tRNA-Try and tRNA-Leu 2 in comparison with the other studied ladybird beetles where the secondary structure of mitochondrial tRNAs was predicted.…”