Morphological characters are compatible with mitogenomic data in resolving the phylogeny of nymphalid butterflies (lepidoptera: papilionoidea: nymphalidae)

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.

Characterization of the complete mitochondrial genome of the Hypolimnas misippus Linnaeus 1764 (Lepidoptera: nymphalidae)

In this study, we sequenced the complete mitochondrial genome (mitogenome) of Hypolimnas misippus Linnaeus 1764, which is 15,283 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an adenine (A) + thymine (T)-rich (D-loop) region. The overall GC level is 19.8%. The phylogenetic position of H. misippus was evaluated using 48 previously published complete mitogenomes, and the results reveals that H. misippus is most closely related to H.bolina.

Exochorion in the tribe Nymphalini (Lepidoptera: Nymphalidae): the genus Hypanartia Hbner, [1821] and comparison with related genera

We describe and compare the exochorion of six species of Hypanartia (H. paullus, H. bella, H. lethe, H. godmanii, H. dione disjuncta, and H. trimaculata autumna) using specimens collected in the field and deposited in entomological collections. We used a standard staining technique and scanning electron microscopy to visualize and describe the main exochorionic characters, especially the ridges and the differentiation in the micropylar, perimicropylar, and transition zones in the apical region. We included plates with photographs, drawings, and schemes for clearer visualization of these structures, which are tabulated for comparison. For our characterization, we considered the ridges in colonnade as the main exochorionic feature in the Nymphalini. Thus, we made brief comparisons of these features among several species of the tribe, particularly with the genus Antanartia. The exochorionic characters agree with the separation of groups (paullus group and dione group). By examining the characteristics of H. paullus, the basal species of the paullus group, we found that ridges with conspicuous columns (e.g., in one section only) appears to be the plesiomorphic state, while those with elongated shafts and walls only in the intercolumn represent the apomorphic state.

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.

The complete mitochondrial genome of Stibochiona nicea (Gray, 1846) (Lepidoptera: Nymphalidae) and phylogenetic analysis

In this study, the complete mitochondrial genome (mitogenome) of Stibochiona nicea (Gray, 1846) (Lepidoptera: Nymphalidae) was first reported with 15,298 bp in size, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes (rrnL and rrnS), and one control region. The nucleotide composition of the entire mitogenome is highly A + T biased (81.5%). The gene content and arrangement of the newly sequenced mitogenome are identical to those of the other available mitogenomes of Nymphalidae. All PCGs start with the conventional ATN codons, except for cox1 initiating with atypical CGA(R). Nine PCGs (atp8, atp6, cox3, nad1, nad2, nad3, nad4l, nad6, and cob) utilize a typical stop codon TAA, whereas the remaining PCGs (cox1, cox2, nad4, and nad5) end with an incomplete stop codon T-. Phylogenetic analysis revealed that S. nicea is closely related to Dichorragia nesimachus within Pseudergolinae, which further forms the sister group to the grouping of (Nymphalinae + (Cyrestinae + (Biblidinae + Apaturinae))). The complete mitogenome of S. nicea will provide useful genetic information for improving the taxonomic system and phylogenetics of Nymphalidae.

Mitogenomes of Eight Nymphalidae Butterfly Species and Reconstructed Phylogeny of Nymphalidae (Nymphalidae: Lepidoptera)

The Nymphalidae family of cosmopolitan butterflies (Lepidoptera) comprises approximately 7200 species found on all continents and in all habitats. However, debate persists regarding the phylogenetic relationships within this family. In this study, we assembled and annotated eight mitogenomes of Nymphalidae, constituting the first report of complete mitogenomes for this family. Comparative analysis of 105 mitochondrial genomes revealed that the gene compositions and orders were identical to the ancestral insect mitogenome, except for Callerebia polyphemus trnV being before trnL and Limenitis homeyeri having two trnL genes. The results regarding length variation, AT bias, and codon usage were consistent with previous reports on butterfly mitogenomes. Our analysis indicated that the subfamilies Limenitinae, Nymphalinae, Apaturinae, Satyrinae, Charaxinae, Heliconiinae, and Danainae are monophyletic, while the subfamily the subfamily Cyrestinae is polyphyletic. Danainae is the base of the phylogenetic tree. At the tribe level, Euthaliini in Limenitinae; Melitaeini and Kallimini in Nymphalinae; Pseudergolini in Cyrestinae; Mycalesini, Coenonymphini, Ypthimini, Satyrini, and Melanitini in Satyrinae; and Charaxini in Charaxinae are regarded as monophyletic groups. However, the tribe Lethini in Satyrinae is paraphyletic, while the tribes Limenitini and Neptini in Limenitinae, Nymphalini and Hypolimni in Nymphalinae, and Danaini and Euploeini in Danainae are polyphyletic. This study is the first to report the gene features and phylogenetic relationships of the Nymphalidae family based on mitogenome analysis, providing a foundation for future studies of population genetics and phylogenetic relationships within this family.

New Complex of Cryptic Species Discovered in Genus Biblis (Papilionoidea: Nymphalidae: Biblidinae) in Mexico

Our research focuses on demonstrating the existence of cryptic species named under Biblis aganisa Boisduval. We used COI sequences to delimit Biblis species for Mexico using species delimitation analyses and examined phylogenetic relationships with sequences from Mexico, Costa Rica, Argentina, USA, and Guana Island using a Bayesian inference tree. We performed a discriminant analysis with quantitative traits using female and male wing and genitalia, and a tree of maximum parsimony based on 39 qualitative characters of wings, head, and male genitalia. The results were congruent in the three analyses. Three groups were formed based on DNA, ECO 01 + DHJ02, ECO 02 + DHJ01, and ECO 03. The characters that contributed over 50% separation were for wings: wing length, anal margin length, and distance from the band to the outer margin; for male genitalia, angle of the integument, uncus, and the length of the hypandrium, while for females, it was the angle of the anteapophysis and the length of the abdomen. For the analysis of qualitative characters, a tree of maximum parsimony was obtained where 20 characters were informative. We confirmed the existence of three cryptic Biblis species in Mexico, two not yet described, and one corresponding to B. aganisa (ECO 02), which is sympatric in Oaxaca and Sinaloa (ECO 03) and in the Yucatan Peninsula (ECO 01).

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.

The complete mitogenome of Habropoda rodoszkowskii (Hymenoptera: Apidae) and phylogenetic analysis

The mitogenome of Habropoda rodoszkowskii, the first complete mitogenome sequence of the genus Habropoda (hymenoptera: Apidae), was sequenced. The mitogenome is 18,497 bp (The proportion of A + T in 80.7%) long, with 37 classic eukaryotic mitochondrial genes (including 13 PCGs, 22 tRNAs, and 2 rRNAs) and an AT-rich region (The proportion of A + T in 78.2%). The Bayesian-inference and Maximum-likelihood phylogenetic relationship was constructed using 15 species from Hymenoptera. According to the phylogenetic tree, Habropoda rodoszkowskii converges with genus Nomada bees (Nomada flava and Nomada flavoguttata) to be supported. In addition, Habropoda rodoszkowskii is more closely related to Apidae than to Megahilidae and Colletidae.

Tick mitochondrial genomes: structural characteristics and phylogenetic implications

Ticks are obligate blood-sucking arachnid ectoparasites from the order Acarina, and many are notorious as vectors of a wide variety of zoonotic pathogens. However, the systematics of ticks in several genera is still controversial. The mitochondrial genome (mt-genome) has been widely used in arthropod phylogeny, molecular evolution and population genetics. With the development of sequencing technologies, an increasing number of tick mt-genomes have been sequenced and annotated. To date, 63 complete tick mt-genomes are available in the NCBI database, and these genomes have become an increasingly important genetic resource and source of molecular markers in phylogenetic studies of ticks in recent years. The present review summarizes all available complete mt-genomes of ticks in the NCBI database and analyses their characteristics, including structure, base composition and gene arrangement. Furthermore, a phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes from ticks. The results will provide important clues for deciphering new tick mt-genomes and establish a foundation for subsequent taxonomic research.

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

Vanessa indica is a small butterfly lacking historical molecular and biological research. Vanessa indica belongs to the family Nymphalidae (Lepidoptera: Papilionoidea), which is the largest group of butterflies and are nearly ubiquitous. However, after more than a century of taxonomic and molecular studies, there is no consensus for family classification, and the phylogenetic relationships within Nymphalidae are controversial. The first objective was to sequence and characterize the complete mitochondrial genome of V. indica. The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae. The mitochondrial genomic DNA (mtDNA) of V. indica was extracted and amplified by polymerase chain reaction. The complete mitochondrial sequence was annotated and characterized by analyzing sequences with SeqMan program. The phylogenetic analyses were conducted on thirteen protein coding genes (PCGs) in 95 mtDNA of Nymphalidae downloaded from GenBank for reference using the maximum likelihood method and Bayesian inference to ensure the validity of the results. The complete mitogenome was a circular molecule with 15,191 bp consisting of 13 protein coding genes, two ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA (tRNA) genes, and an A + T-rich region (D-loop). The nucleotide composition of the genome was highly biased for A + T content, which accounts for 80.0% of the nucleotides. All the tRNAs have putative secondary structures that are characteristic of mitochondrial tRNAs, except tRNA^Ser(AGN). All the PCGs started with ATN codons, except cytochrome c oxidase subunit 1 (COX1), which was found to start with an unusual CGA codon. Four genes were observed to have unusual codons: COX1 terminated with atypical TT and the other three genes terminated with a single T. The A + T rich region of 327 bp consisted of repetitive sequences, including a ATAGA motif, a 19-bp poly-T stretch, and two microsatellite-like regions (TA)₈. The phylogenetic analyses consistently placed Biblidinae as a sister cluster to Heliconiinae and Calinaginae as a sister clade to Satyrinae. Moreover, the phylogenetic tree identified Libytheinae as a monophyletic group within Nymphalidae. The complete mitogenome of V. indica was 15,191 bp with mitochondrial characterizations common for lepidopteran species, which enriched the mitochondria data of Nymphalid species. And the phylogenetic analysis revealed different classifications and relationships than those previously described. Our results are significant because they would be useful in further understanding of the evolutionary biology of Nymphalidae.

The complete mitochondrial genome of the Sideridis albicosta (Lepidoptera: Noctuoidea: Noctuidae)

The complete mitochondrial genome (mitogenome) of Sideridis albicosta is described in this study. The circular molecule is 15,320 bp in length and contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one AT-rich region. Thirteen PCGs is 11,252 bp in total, encoding 3723 amino acids. All PCGs start with ATN, except for COI gene starting with CGA; 10 of the 13 PCGs use the typical stop codon TAA, whereas COI, COII, and ND4 stop with a single T. The rrnL and rrnS genes are 1377 bp and 783 bp in length, respectively. The 328 bp AT-rich region contains several structures characteristic of the lepidopterans. New phylogenetic analyses upon mitogenomics would provide us further insights on the taxonomy and phylogeny of Noctuoidea.

The complete mitochondrial genome of Pidorus atratus (Lepidoptera: Zygaenoidea: Zygaenidae)

The complete mitochondrial genome (mitogenome) of Pidorus atratus (Lepidoptera: Zygaenoidea: Zygaenidae) is described in this study. The circular molecule is 15,383 bp in length and contains 37 typical mitochondrial genes and one non-coding AT-rich region. All protein-coding genes (PCGs) start with ATN, except for cox1 gene with CGA; 10 of the 13 PCGs harbour the typical stop codon TAA, whereas cox1, cox2, and nad4 end with a single T. Two ribosomal RNA genes (rRNAs) are 1366 bp and 544 bp in length, respectively. The AT-rich region is 658 bp in size and harbours several features characteristic of the lepidopterans, including the motif ATAGA followed by a 20 bp poly-T stretch and a microsatellite-like (TA)9 element. The complete mitogenome data would be useful for further understanding the taxonomy and phylogeny of Zygaenoidea.

Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes

DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.

The complete mitochondrial genome of comma, polygonia c-aureum (Lepidoptera: Nymphalidae: Nymphalinae)

The mitochondrial genome (mitogenome) of Polygonia c-aureum (Lepidoptera: Nymphalidae: Nymphalinae) is determined to be 15,209 bp in length and shows AT bias (80.6%). Similar to other butterflies, it contains 37 typical mitochondrial genes and one AT-rich region (D-loop). All protein-coding genes (PCGs) started with ATN, except for cox1 gene with CGA(R), which is often found in other butterflies, and seven PCGs harbour the typical stop codon TAA, whereas cox1, cox2, nad3, nad5, nad4 and nad1 end with a single T. The rrnL and rrnS genes are 1332 bp and 773 bp in length, respectively. The 342 bp AT-rich region contains non-repetitive sequences, but harbour several features common to the lepidopterans, including the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element preceded by the ATTTA motif. The complete mitogenome sequence provided here would be useful for further understanding the taxonomy and phylogeny of Nymphalinae.

The complete mitochondrial genome of Damora sagana and phylogenetic analyses of the family Nymphalidae

The monotypic genus Damora (Nymphalidae, Heliconiinae) contains a single species, Damora sagana, which is widely distributed across southern China. Herein, its complete mitogenome was sequenced to further understand lepidopteran mitogenome characteristics, reconstruct the nymphalid family phylogeny, and infer the subdivision of Heliconiinae species. The circular mitogenome was 15,151 bp long, abundant in A and T, and comprised of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one control region with a gene arrangement typical of lepidopteran mitogenomes. ATN codons initiated all PCGs, except cytochrome c oxidase subunit 1 (COX1), which was initiated by a CGA sequence as has been observed in other lepidopterans. Three PCGs (COX1, COX2 and ND4) employed a single T termination signal, whereas others had the typical complete termination codon (TAA). All tRNA genes were folded into the typical cloverleaf structure except for tRNA-Ser (AGN). The A+T-rich region included the conserved motif 'ATAGA' followed by a 17 bp poly-T stretch, which was also observed in tribe Argynnini mitogenomes. A phylogenetic tree was constructed via multiple methods using the 13 PCGs data of D. sagana and other available mitogenomes of nymphalid species. All three phylogenetic trees yielded the same topology. These results were consistent with those from previous studies of most major nymphalid groups, except those regarding tribe subdivision in certain subfamilies such as Argynnini + (Acraeini + Heliconiini) for Heliconiine. Furthermore, our analyses identified that the genus Cethosia was grouped with the genus Acraea composing the tribe Acraeini with strong support.

Dated phylogeny and dispersal history of the butterfly subfamily Nymphalinae (Lepidoptera: Nymphalidae)

The origin and dispersal history of the large butterfly subfamily Nymphalinae are not fully understood, due to internal phylogenetic and time calibration issues. We conducted phylogenetic and dating analyses using mitochondrial and nuclear genes of biogeographically diverse groups of the Nymphalinae in order to resolve some controversial relationships and the paleobiogeographic pattern of the subfamily. Our results support the sister relationship of Vanessa (Tribe Nymphalini) and the Nymphalis-group, and the grouping of the three old-world genera (Rhinopalpa, Kallimoides and Vanessula) within Tribe Victorinini. Molecular dating analyses invoking two additional calibrations under the butterfly-host plant coevolutionary scenarios result in a relatively deeper divergence of the subfamily's two major clades (Nymphalini and the Kallimoids), compatible with the Cretaceous floral turnover scenario during the so-called Cretaceous Terrestrial Revolution. Phylobiogeographic analyses reveal that the Oriental region is probably the center of early divergences for Nymphalinae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by repeated dispersals into the rest of the Old World and the New World during various periods beginning in Eocene. The biogeographic history indicates that temperature changes and host-plant diversification may have facilitated the dispersals of this butterfly subfamily, with accelerated global colonization during the middle to late Miocene.

Sequencing and characterization of the Megachile strupigera (Hymenoptera: Megachilidae) mitochondrial genome

The mitochondrial genome (mitogenome) of Megachile strupigera (Hymenoptera: Megachilidae: Megachilinae) was determined in our study. The sequenced region is 15,193 bp with an A + T content of 83.44%, including 13 protein-coding genes, two ribosomal RNAs and 19 transfer RNAs. All PCGs are initiated by typical ATN codons and stop with the complete termination codon TAA, except for nad3 gene, which has an incomplete stop codon T. Bayesian method supported the monophyly of both Megachilidae and Apoidea. And within the Apoidea, Apidae and Megachilidae formed a sister clade to Colletidae.