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The nymphalid butterfly genus Junonia has remarkable dispersal abilities. Occurring on every continent except Europe and Antarctica, Junonia are often among the only butterflies on remote oceanic islands. The biogeography of Junonia has been controversial, plagued by taxonomic disputes, small phylogenetic datasets, incomplete taxon sampling, and shared interspecific mitochondrial haplotypes. Junonia originated in Africa but its route into the New World remains unknown. Presented here is, to our knowledge, the most comprehensive Junonia phylogeny to date, using full mitogenomes and nuclear ribosomal RNA repeats from 40 of 47 described species. Junonia is monophyletic and the genus Salamis is its probable sister clade. Genetic exchange between Indo-Pacific Junonia villida and New World Junonia vestina is evident, suggesting a trans-Pacific route into the New World. However, in both phylogenies, the sister clades to most New World Junonia contain both African and Asian species. Multiple trans-Atlantic or trans-Pacificinvasions could have contributed to New World diversification. Hybridization and lateral transfer of mitogenomes, already well-documented in New World Junonia, also occurs in at least two Old World lineages (Junonia orithya/Junonia hierta and Junonia iphita/Junonia hedonia). Variation associated with reticulate evolution creates challenges for phylogenetic reconstruction, but also may have contributed to patterns of speciation and diversification in this genus.

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The file ramshorn snail Planorbella pilsbryi Baker, 1926 (Gastropoda: Hygrophila: Planorbidae) is a widespread herbivorous North American freshwater snail found in diverse habitats, including standing and moving water bodies. Genome skimming by Illumina sequencing allowed the assembly of a complete nuclear rRNA repeat sequence and a complete circular mitogenome of 13,720 bp from P. pilsbryi consisting of 75.3% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the typical order found in panpulmonate snails. Planorbella pilsbryi COXI features a rare TTG start codon while COXII, CYTB, ND2, ND3, and ND5 exhibit incomplete stop codons completed by the addition of 3' A residues to the mRNA. Phylogenetic reconstruction of mitochondrial protein-coding gene and rRNA sequences places P. pilsbryi as sister taxon to Planorbella duryi (Planorbidae) within family Planorbidae, which is consistent with previous phylogenetic hypotheses.

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The peacock butterfly Aglais io (Linnaeus, 1758) (Nymphalidae: Nymphalinae: Nymphalini) is a colorful and charismatic flagship butterfly species whose range spans from the British Isles and Europe through temperate Asia and the Far East. In Europe, it has been used as a model species for studying the effects of GMO maize pollen on caterpillar growth and survivorship. The Japanese subspecies, Aglais io geisha (Stichel 1907), is not as well studied as its European counterpart. Genome skimming by Illumina sequencing allowed the assembly of a complete circular mitochondrial genome (mitogenome) of 15,252 bp from A. io geisha consisting of 80.6% AT nucleotides, 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region in the gene order typical of butterfly species. Aglais io geisha COX1 gene features an atypical start codon (CGA) while COX1, COX2, CYTB, ND1, ND3, ND4, and ND5 display incomplete stop codons finished by the addition of 3' A residues to the mRNA. Bayesian phylogenetic reconstruction places A. io geisha within a clade with European A. io mitogenomes in the tribe Nymphalini, which is consistent with previous phylogenetic hypotheses.

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The Blomfild's Beauty butterfly Smyrna blomfildia (Fabricius 1781) (Lepidoptera: Nymphalidae: Nymphalini) is a sexually dimorphic species found in Mexico, Central, and South America. Males are territorial and are more vibrantly colored than females. Genome skimming by Illumina sequencing allowed the assembly of a complete circular mitochondrial genome (mitogenome) of 15,149 bp from S. blomfildia consisting of 83.9% AT nucleotides, 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region in the typical butterfly gene order. The S. blomfilda COX1 gene features an atypical start codon (CGA) while ATP6, COX1, COX2, CYTB, ND1, ND3, ND4, and ND5 display partial stop codons completed by the addition of 3' A residues to the mRNA. Bayesian phylogenetic reconstruction places Smyrna as a member of the tribe Nymphalini and sister to a clade containing genera Araschnia, Vanessa, Polygonia, and Aglais, which differs from its classic taxonomic placement in tribe Coeini.

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Butterfly wing color patterns are a representative model system for studying biological pattern formation, due to their two-dimensional simple structural and high inter- and intra-specific variabilities. Moreover, butterfly color patterns have demonstrated roles in mate choice, thermoregulation, and predator avoidance via disruptive coloration, attack deflection, aposematism, mimicry, and masquerade. Because of the importance of color patterns to many aspects of butterfly biology and their apparent tractability for study, color patterns have been the subjects of many attempts to model their development. Early attempts focused on generalized mechanisms of pattern formation such as reaction-diffusion, diffusion gradient, lateral inhibition, and threshold responses, without reference to any specific gene products. As candidate genes with expression patterns that resembled incipient color patterns were identified, genetic regulatory networks were proposed for color pattern formation based on gene functions inferred from other insects with wings, such as Drosophila. Particularly detailed networks incorporating the gene products, Distal-less (Dll), Engrailed (En), Hedgehog (Hh), Cubitus interruptus (Ci), Transforming growth factor-ß (TGF-ß), and Wingless (Wg), have been proposed for butterfly border ocelli (eyespots) which helps the investigation of the formation of these patterns. Thus, in this work, we develop a mathematical model including the gene products En, Hh, Ci, TGF-ß, and Wg to mimic and investigate the eyespot formation in butterflies. Our simulations show that the level of En has peaks in the inner and outer rings and the level of Ci has peaks in the inner and middle rings. The interactions among these peaks activate cells to produce white, black, and yellow pigments in the inner, middle, and outer rings, respectively, which captures the eyespot pattern of wild type Bicyclus anynana butterflies. Additionally, our simulations suggest that lack of En generates a single black spot and lack of Hh or Ci generates a single white spot, and a deficiency of TGF-ß or Wg will cause the loss of the outer yellow ring. These deficient patterns are similar to those observed in the eyespots of Vanessa atalanta, Vanessa altissima, and Chlosyne nycteis. Thus, our model also provides a hypothesis to explain the mechanism of generating the deficient patterns in these species.

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The Indian leafwing butterfly Kallima paralekta (Horsfield, 1829) (Nymphalidae) is an Asian forest-dwelling, leaf-mimic. Genome skimming by Illumina sequencing permitted assembly of a complete circular mitogenome of 15,200 bp from K. paralekta consisting of 79.5% AT nucleotides, 22 tRNAs, 13 protein-coding genes, two rRNAs and a control region in the typical butterfly gene order. Kallima paralekta COX1 features an atypical CGA start codon, while ATP6, COX1, COX2, ND4, ND4L, and ND5 exhibit incomplete stop codons completed by 3' A residues added to the mRNA. Phylogenetic reconstruction places K. paraleckta within the monophyletic genus Kallima, sister to Mallika in the subfamily Nymphalinae. These data support the monophyly of tribe Kallimini and contribute to the evolutionary systematics of the Nymphalidae.

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The taxonomic placement of the moth-butterfly, Macrosoma conifera (Warren 1897) (Lepidoptera: Hedylidae), has been controversial. The 15,344 bp complete M. conifera circular mitogenome, assembled by genome skimming, consists of 81.7% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the typical butterfly gene order. Macrosoma conifera COX1 features an atypical CGA start codon while ATP6, COX1, COX2, and ND5 exhibit incomplete stop codons completed by the post-transcriptional addition of 3' A residues. Phylogenetic reconstruction places M. conifera as sister to the skippers (Hesperiidae), which is consistent with several recent phylogenetic analyses.

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The white peacock butterfly Anartia jatrophae saturata Staudinger, 1884 (Nymphalidae: Nymphalinae: Victorini), lives in the neotropics. Genome skimming with Illumina sequencing of A. jatrophae saturata allowed the assembly of a complete circular mitogenome of 15,297 bp, consisting of 81.4% AT nucleotides, 22 tRNAs, 13 protein-coding genes, two rRNAs, and a control region. Anartia jatrophae COX1 features an atypical start codon (CGA); ATP6, COX1, ND1, ND4, ND4L, ND5, and ND6 exhibit incomplete stop codons completed in the mRNA by the addition of 3' A residues. Contrary to previous phylogenetic hypotheses, phylogenetic reconstruction places A. jatrophae as sister to nymphalid tribe Nymphalini.

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The Malagasy clouded mother-of-pearl butterfly, Protogoniomorpha ancardii duprei (Nymphalidae), is the Madagascar subspecies of a widespread sub-Saharan leaf-mimic. Genome skimming allowed the assembly of the complete P. ancardii duprei circular mitogenome (15,220 bp) consisting of 80% AT nucleotides, 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region in typical butterfly gene order. Protogoniomorpha ancardii duprei COX1 has a CGA start codon while COX1, COX2, CYTB, NAD1, and NAD4 exhibit partial stop codons completed by 3' A residues added to the mRNA. Phylogenetic reconstruction places Protogoniomorpha as sister to genus Yoma within monophyletic tribe Junoniini.

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The European map butterfly Araschnia levana (Linnaeus, 1758) is a species showing extreme seasonal polyphenism. The complete 15,207 bp circular A. levana mitogenome consisting of 81.6% AT nucleotides, was assembled by Illumina genome skimming. It includes 22 tRNAs, 13 protein-coding genes, 2 rRNAs, and a control region in the typical butterfly gene order. Araschnia levana COX1 features an atypical CGA start codon and ATP6, COX1, COX2, ND1, ND3, and ND4 have incomplete stop codons completed by 3'A residues added to the mRNA. Phylogenetic reconstruction places A. levana as a basal lineage within tribe Nymphalini, consistent with previous phylogenetic hypotheses.

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The Jackson's leaf butterfly Mallika jacksoni (Sharpe 1896), is a leaf-mimicking species from tropical East Africa. Genome skimming by Illumina sequencing permitted the assembly of the complete circular M. jacksoni 15,183 bp mitogenome. It consists of 79.4% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs, and a control region in the typical butterfly gene order. Mallika jacksoni COX1 has a CGA start codon while ATP6, COX1, COX2, ND3, ND4, and ND5 exhibit partial stop codons completed by 3'-A residues added to the mRNA. Phylogenetic reconstruction places M. jacksoni as sister to Kallima within nymphalid tribe Kallimini.

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Here we reply to the "Refutation" of Lawrence, Casal, de Cellis, and Morata, who critique our paper presenting evidence for an organizer and compartment boundary subdividing the widely recognized posterior wing compartment of butterflies and moths (Lepidoptera) and Drosophila, that we called the F-P boundary. Lawrence et al. present no data from the Lepidoptera and while the data that they present from Drosophila melanogaster mitotic clones are intriguing and may be informative with respect to the timing of the activity of the A-P and F-P organizers, considerable ambiguity remains regarding how their data should be interpreted with respect to the proposed wing compartment boundaries. Thus, contrary to their claims, Lawrence et al. have failed to falsify the F-P boundary hypothesis. Additional studies employing mitotic clones labeled with easily detectable markers that do not affect cytoskeletal organization or rates of cell division such as GFP and RFP clones produced by G-Trace or Twin Spot Generator (TSG) may further clarify the number of compartment boundaries in Drosophila wings. At the same time, because Drosophila wings are diminutive and highly modified compared to other insects, we also urge great caution in making generalizations about insect wing development based exclusively on studies in Drosophila.Replying to: Lawrence, P.A., Casal, J., de Celis, J., Morata, G. A refutation to 'A new A-P compartment boundary and organizer in holometabolous insect wings'. Sci. Rep. 9 (2019), https://doi.org/10.1038/s41598-019-42668-y .

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The brown pansy, Junonia stygia (Aurivillius, 1894) (Lepidoptera: Nymphalidae), is a widespread West African forest butterfly. Genome skimming by Illumina sequencing allowed assembly of a complete 15,233 bp circular mitogenome from J. stygia consisting of 79.5% AT nucleotides. Mitochondrial gene order and composition is identical to other butterfly mitogenomes. Junonia stygia COX1 features an atypical CGA start codon, while ATP6, COX1, COX2, ND4, and ND4L exhibit incomplete stop codons. Phylogenetic reconstruction supports a monophyletic Subfamily Nymphalinae, Tribe Junoniini, and genus Junonia. The phylogenetic tree places Junonia iphita and J. stygia as basal mitogenome lineages sister to the remaining Junonia sequences.

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Frequent exposure of plants to solar ultraviolet radiation (UV) results in damaged DNA. One mechanism of DNA repair is the light independent pathway Global Genomic Nucleotide Excision Repair (GG-NER), which repairs UV damaged DNA throughout the genome. In mammals, GG-NER DNA damage recognition is performed by the Damaged DNA Binding protein 1 and 2 (DDB1/2) complex which recruits the Xeroderma Pigmentosa group C (XPC) / RAD23D complex. In the yeast Saccharomyces cerevisiae, distinct proteins, Radiation sensitive 7 and 16 (Rad7p and Rad16p), recognize the damaged DNA strand and then recruit the XPC homologue, Rad4p, and Rad23p. The remainder of the proteins involved GG-NER are well conserved. DDB1, DDB2, XPC/RAD4, and RAD23 homologues have been described in the model plant Arabidopsis thaliana. In this study we characterize three Arabidopsis RAD7 homologues, RAD7a, RAD7b, and RAD7c. Loss of function alleles of each of the three RAD7 homologues result in increased UV sensitivity. In addition, RAD7b and RAD7c overexpression lines exhibited increased UV tolerance. Thus RAD7 homologues contribute to UV tolerance in plants as well as in yeast. This is the first time any system has been shown to utilize both the DDB1/2 and RAD7/16 damage recognition complexes.

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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.

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Decades of research on the highly modified wings of Drosophila melanogaster has suggested that insect wings are divided into two Anterior-Posterior (A-P) compartments separated by an axis of symmetry. This axis of symmetry is created by a developmental organizer that establishes symmetrical patterns of gene expression that in turn pattern the A-P axis of the wing. Butterflies possess more typical insect wings and butterfly wing colour patterns provide many landmarks for studies of wing structure and development. Using eyespot colour pattern variation in Vanessa butterflies, here we show an additional A-P axis of symmetry running between wing sectors 3 and 4. Boundaries of Drosophila mitotic clones suggest the existence of a previously undetected Far-Posterior (F-P) compartment boundary that coincides with this additional A-P axis. A similar compartment boundary is evident in butterfly mosaic gynandromorphs. We suggest that this additional compartment boundary and its associated developmental organizer create an axis of wing colour pattern symmetry and a gene expression-based combinatorial code, permitting each insect wing compartment to acquire a unique identity and allowing for the individuation of butterfly eyespots.

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The caddisfly Anabolia bimaculata, is a rapidly-maturing caddisfly found in temporary ponds across western North America. Whole genome Illumina sequencing facilitated the assembly of a complete circular mitochondrial genome of 15,048 bp from A. bimaculata consisting of 78.2% AT nucleotides, 22 tRNAs, 13 protein-coding genes, two rRNAs and a control region arranged in the canonical and ancestral gene order found in insects. This gene order is consistent with the gene order found in most other caddisfly species. Maximum likelihood phylogenetic reconstruction places A. bimaculata within a monophyletic Order Trichoptera and sister to the primitive lepidopteran Micropterix calthella (Micropterigidae).

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The long-horned caddisfly Triaenodes tardus Milne, 1934 (Leptoceridae), is a widespread herbivorous North American caddisfly found in both lentic and lotic habitats. Whole genome Illumina sequencing allowed the assembly of a complete circular mitogenome of 14,963 bp from T. tardus consisting of 73.4% AT nucleotides, 22 tRNAs, 13 protein-coding genes, two rRNAs and a control region in the ancestral insect gene order. Triaenodes tardus COX1 features an atypical TTG start codon as in some lepdioptera and prokaryotes. Phylogenetic reconstruction places T. tardus as sister to Sericostoma personatum (Sericostomatidae) within a monophyletic Order Trichoptera, which is consistent with previous phylogenetic hypotheses.

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The Bermuda buckeye, Junonia coenia bergi, is the only butterfly endemic to Bermuda, but is largely unstudied. Whole-genome Illumina sequencing was used to obtain a complete circular mitochondrial genome sequence of 15,221 bp consisting of 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region. Mitogenome structure and organization was found to be very similar to that of other Junonia butterfly mitogenomes. Excluding ambiguous nucleotides, the J. coenia bergi mitogenome is 99.1% identical to the J. coenia coenia mitogenome. Parsimony and maximum-likelihood phylogenetic reconstruction revealed the monophyly of subfamily Nymphalinae, genus Junonia, and species J. coenia.

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The New World Junonia butterflies are a possible ring species with a circum-Caribbean distribution. Previous reports suggest a steady transition between North and South American forms in Mesoamerica, but in Cuba the forms were thought to co-exist without interbreeding representing the overlapping ends of the ring. Three criteria establish the existence of a ring species: a ring-shaped geographic distribution, gene flow among intervening forms, and genetic isolation in the region of range overlap. We evaluated mitochondrial cytochrome oxidase I haplotypes in Junonia from 9 species in the Western Hemisphere to test the Junonia ring species hypothesis. Junonia species are generally not monophyletic with respect to COI haplotypes, which are shared across species. However, two major COI haplotype groups exist. Group A predominates in South America, and Group B predominates in North and Central America. Therefore, COI haplotypes can be used to assess the degree of genetic influence a population receives from each continent. Junonia shows a ring-shaped distribution around the Caribbean, and evidence is consistent with gene flow among forms of Junonia, including those from Mesoamerica. However, we detected no discontinuity in gene flow in Cuba or elsewhere in the Caribbean consistent with genetic isolation in the region of overlap. Though sampling is still very limited in the critical region, the only remaining possiblity for a circum-Caribbean discontinuity in gene flow is at the Isthmus of Panama, where there may be a transition from 98% Group B haplotypes in Costa Rica to 85-100% Group A haplotypes in South America.