The complete mitochondrial genome of Vanessa indica and phylogenetic analyses of the family Nymphalidae

Characterization of the Complete Mitochondrial Genome of Three Satyrid Butterfly Species (Satyrinae:Amathusiini) and Reconstructed Phylogeny of Satyrinae

Satyrinae, one of the most species-rich groups within the Nymphalidae family, has traditionally relied on morphological characteristics for classification. However, this approach encounters challenges due to issues such as cryptic species and paraphyletic groups. Recent molecular phylogenetic studies have revealed the complex evolutionary history of Satyrinae, leading to the reclassification of the originally polyphyletic Satyrini into multiple independent tribes and confirming the monophyletic status of groups such as Amathusiini. Nevertheless, the phylogenetic relationships and divergence times of certain tribes remain contentious. This study focuses on three species of the Amathusiini tribe (Faunis aerope, Stichophthalma howqua, and Aemona lena), constructing a phylogenetic tree by sequencing the complete mitochondrial genome and integrating 13 protein-coding genes, including COI and ND5. The results indicate that the mitogenome lengths for the three satyrid species are 15,512 bp for Faunis aerope, 13,914 bp for Stichophthalma howqua, and 15,288 bp for Aemona lena. The genetic composition and sequencing of the newly obtained mitogenomes exhibit high conservation and are distinctive to this group of butterflies. Each of the three mitogenomes contains a characteristic collection of 37 genes along with an AT-rich region. Notably, the tRNA genes across these mitogenomes display a conventional cloverleaf configuration; however, the tRNASer stem (AGN) lacks the dihydrouridine (DHU) arm. The three species exhibit varying lengths of AT-rich regions, resulting in differences in their mitochondrial genome sizes. Finally, the phylogenetic analysis supports the relationships among the four tribes of Satyrinae as: (Satyrini + (Amathusiini + Elymniini)) + Melanitini.

Phylogenetic and Comparative Genomics Study of Papilionidae Based on Mitochondrial Genomes

Most species of Papilionidae are large and beautiful ornamental butterflies. They are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. Complete mitochondrial genomes (mitogenomes) have been widely used in phylogenetic studies of butterflies, but mitogenome knowledge within the family Papilionidae is limited, and its phylogeny is far from resolved. In this study, we first report the mitogenome of Byasa confusa from the subfamily Papilioninae of Papilionidae. The mitogenome of B. confusa is 15,135 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region (CR), closely mirroring the genomic structure observed in related butterfly species. Comparative analysis of 77 Papilionidae mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, Ka/Ks, and relative synonymous codon usage (RSCU) are all consistent with that of other reported butterfly mitogenomes. We conducted phylogenetic analyses using maximum-likelihood (ML) and Bayesian-inference (BI) methods, with 77 Papilionidae species as ingroups and two species of Nymphalidae and Lycaenidae as outgroups. The phylogenetic analysis indicated that B. confusa were clustered within Byasa. The phylogenetic trees show the monophyly of the subfamily Papilioninae and the tribes Leptocircini, Papilionini, and Troidini. The data supported the following relationships in tribe level on Papilioninae: (((Troidini + Papilionini) + Teinopalpini) + Leptocircini). The divergence time analysis suggests that Papilionidae originated in the late Creataceous. Overall, utilizing the largest number of Papilionidae mitogenomes sequenced to date, with the current first exploration in a phylogenetic analysis on Papilionidae (including four subfamilies), this study comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of the Papilionidae family.

Characterization of the complete mitochondrial genome of an endemic species in China, Aulocera merlina (Lepidoptera: Nymphalidae: Satyrinae) and phylogenetic analysis within Satyrinae

The mitochondrial genome (mitogenome) has been extensively used as molecular markers in determining the insect phylogenetic relationships. In order to resolve the relationships among tribes and subtribes of Satyrinae at the mitochondrial genomic level, we obtained the complete mitogenome of Aulocera merlina (Oberthür, 1890) (Lepidoptera: Nymphalidae: Satyrinae) with a size of 15,259 bp. The mitogenome consisted of 37 typical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. The gene organization and arrangement were similar to those of all other known Satyrinae mitogenomes. All PCGs were initiated with the canonical codon pattern ATN, except for the cox1 gene, which used an atypical CGA codon. Nine PCGs used the complete stop codon TAA, while the remaining PCGs (cox1, cox2, nad4, and nad5) were terminated with a single T nucleotide. The canonical cloverleaf secondary structures were found in all tRNAs, except for trnS1 which lacked a dihydrouridine arm. The 448 bp A + T-rich region was located between rrnS and trnM, and it included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)6 element preceded by the ATTTA motif. The phylogenetic tree, inferred using Bayesian inference and maximum likelihood methods, generated similar tree topologies, revealing well-supported monophyletic groups at the tribe level and recovering the relationship ((Satyrini + Melanitini) + ((Amathusiini + Elymniini) + Zetherini)). The close relationship between Satyrina and Melanargiina within the Satyrini was widely accepted. Additionally, Lethina, Parargina, and Mycalesina were closely related and collectively formed a sister group to Coenonymphina. Moreover, A. merlina was closely related to Oeneis buddha within the Satyrina. These findings will provide valuable information for future studies aiming to elucidate the phylogenetic relationships of Satyrinae.

Mitogenomic phylogeny of nymphalid subfamilies confirms the basal clade position of Danainae (Insecta: Lepidoptera: Nymphalidae)

The phylogenetic relationships among the nymphalid subfamilies have largely been resolved using both morphological and molecular datasets, with the exception of a conflicting basal clade position for Libytheinae or Danainae that remains contentious between morphological and molecular studies. Several phylogenomic analyses have found that the danaine clade is sister to other nymphalid subfamilies; however, it largely depends on utilizing different molecular datasets, analysis methods, and taxon sampling. This study aimed to resolve the basal clade position and relationships among subfamilies and tribes of Nymphalinae by combining the most comprehensive available mitogenomic datasets with various analyses methods by incorporating a new Symbrenthia lilaea Hewitson sequence data. Phylogenetic relationships among 11 nymphalid subfamilies and the tribes of Nymphalinae were inferred by combining new and available mitogenomic sequence data from 80 ingroup and six outgroup species. The phylogenetic trees were reconstructed using maximum-likelihood (ML) and Bayesian inference (BI) methods based on five concatenated datasets: amino acid sequences and nucleotides from different combinations of protein-coding genes (PCGs), ribosomal RNA (rRNAs), and transfer RNA (tRNAs). Danainae is well-supported as the basal clade and sister to the remaining nymphalid subfamilies, except for the paraphyletic Libytheinae. Libytheinae was either recovered as a sister to the danaine clade followed by the satyrine clade or sister to the nymphaline + heliconiine clades, and is consistent with recent phylogenetic studies on Nymphalidae. The monophyletic Nymphalinae has been recovered in all analyses and resolves tribal-level relationships with high support values in both BI and ML analyses. We supported the monophyletic Nymphalini as a sister clade to Victorini, Melitaeini, and Kallimini + Junoniini with high supporting values in BI and ML analyses, which is consistent with previously published morphological and molecular studies.

Complete mitochondrial genome of the summer heath fritillary butterfly, Mellicta ambigua (Lepidoptera: Nymphalidae)

We sequenced the mitochondrial genome (mitogeome) of the summer heath fritillary bullterfly, Mellicta ambigua Ménétriès, 1859 (Lepidoptera: Nymphalidae), which is listed as an endangered insect in South Korea. The 15,205-bp long complete genome contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 A + T-rich region with an arrangement identical to that observed in most insect mitogenomes. Unlike the other PCGs, COI had the atypical CGA start codon frequently found in lepidopteran COI. The A/T content of the whole mitogenome was 80.57%; however, it varied among the regions/genes as follows: A + T-rich region, 93.39%; srRNA, 85.37%; lrRNA, 84.92%; tRNAs, 81.13%; and PCGs, 79.22%. Phylogenetic analyses using concatenated sequences of the 13 PCGs and 2 rRNAs placed M. ambigua as a sister group to the within-tribe species, Melitaea cinxia, with the highest nodal support both in the maximum-likelihood (ML) and Bayesian inference (BI) methods.

Fourteen complete mitochondrial genomes of butterflies from the genus Lethe (Lepidoptera, Nymphalidae, Satyrinae) with mitogenome-based phylogenetic analysis

The mitochondrial genome (mitogenome) can help us understand the phylogenetic relationships within the genus Lethe and the subfamily Satyrinae. In this study, we sequenced the complete mitogenomes of 14 Lethe species, which range in size from 15,225 to 15,271 bp, with both 37 genes (13 PCGs, 22 tRNAs, 2 rRNAs) and a noncoding A + T-rich region. The gene arrangement and orientation is similar to typical mitogenomes of Lepidoptera. The Ka/Ks ratio shows that cox1 has the slowest evolutionary rate. The secondary structure of trnN lacks the Pseudouracil loop (TψC loop) in most Lethe species. The inferred phylogenetic analyses show that Lethe is a well-supported monophyletic group, and reveal 2 major clades within the genus Lethe, which is consistent with previous morphological classifications.

Complete mitochondrial genome of two Thitarodes species (Lepidoptera, Hepialidae), the host moths of Ophiocordyceps sinensis and phylogenetic implications

Thitarodes (Lepidoptera, Hepialidae) is the only genus that hosts to the Ophiocordyceps sinensis, a traditional Chinese medicine considered as a powerful medicinal supplement. In this study, the complete mitochondrial genomes (mitogenomes) of two species, T. damxungensis and T. pui, have been sequenced, which are 15,928 bp and 15,362 bp in size respectively, and both contain 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and an AT-rich region. Like other hepialoids, the gene arrangement of the mitogenomes of T. damxungensis and T. pui is identical to the ancestral arrangement but differs from those of other lepidopteran species on account of the different arrangements of trnM, trnI, and trnQ. The size of AT-rich region is 545 bp in T. damxungensis and 1030 bp in T. pui. Tandem repetition in the AT-rich region is responsible for the length difference of the A + T-rich region in both species. In Hepialidae, the phylogenetic study based on the dataset of the sequences that combined the protein-coding genes and RNA genes suggested that the species T. yunnanensis should still belong to the genus Thitarodes rather than Ahamns, which is different from the results based on the traditional phylogeny.