Search

Aim: Knowledge of taxonomy and species distributions in highly diverse lineages of invertebrates remains too incomplete for the study of biogeographical patterns at the global scale. This limits the understanding of processes leading to the formation and maintenance of boundaries between major biogeographical realms. Site‐based metagenomic approaches may provide an alternative source of data for inference of historical processes of in situ speciation and interchange among biogeographical regions. We applied the methodology to explore the historical biogeography of the Qinling Mountains at the boundary of the Oriental and Palaearctic regions. Location: The focal area in the Qinling Mountains; sites in Borneo, Panama, and Spain, representing the Oriental, Neotropical and Palaearctic faunas. Time Period: Contemporary. Major Taxa Studied: Chrysomelidae, a group of ~40,000 species with worldwide distribution. Methods: Mass‐trapped insects were subjected to deep Illumina DNA sequencing and mitochondrial genome assembly, followed by phylogenetic analysis and historical biogeographical inference on a dated tree. The methodology produced 622 mitogenomes (304 newly sequenced) each representing a morphologically distinct species. Results: Ancestral area reconstruction revealed that the Qinling fauna is a composite of distinct clades that, respectively, have Oriental or Palaearctic ancient origins, while in situ speciation and local clade formation were limited. The global diversity of Chrysomelidae consists of regionalised deep clades at the level of the major zoogeographic realms, which remain recognisable where these realms abut in the Qinling mountains. Yet, the Qinling fauna is clearly distinct from the source areas although local lineage ages are generally <20 Ma. Main Conclusions: The Qinling fauna is a composite of clades that have either Oriental or Palaearctic origin, indicating the important role of immigration at the realm boundary. Global site‐based phylogenetic analyses based on metagenomic sequencing can address previously intractable questions about the historical biogeography of poorly studied groups even without a fully developed taxonomy. [ABSTRACT FROM AUTHOR]

Simple Summary: Monolepta is one of the largest groups in the subfamily Galerucinae, which has considerable ecological and economic significance. However, the lack of mitogenomic data for Monolepta limits our understanding of the taxonomy and phylogeny of this genus. Here, the completed mitogenomes of four Monolepta species were obtained using high-throughput sequencing technology. We compared the main features of newly sequenced mitogenomes, as well as the rate of evolution, base compositions, and relative synonymous codon usage (RSCU) of the mitogenomes among Monolepta species. Furthermore, combined with all available mitochondrial genomes and ND1 data, the relationships of the section "Monoletites" at the suprageneric and species levels were explored. The section "Monoleptites" was proved to be a monophyletic group, while Monolepta was a non-monophyletic group. This study supported that the characteristic of "antennal segment 2 equals 3" of the true "Monolepta" evolved multiple times in several subgroups. This study will provide the basal data for further study of the taxonomy and phylogeny of Galerucinae. Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome ofJaponica luteais 15,225 bp in length, containing 37 typical insect genes: 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. All the 13 PCGs are initiated with ATN, except for COI gene which is started by CGA. Nine PCGs use the complete termination codon (TAN), whereas the COI, COII, ND4 and ND5 genes end with single nucleotide T. In total, 131 bp intergenic spacers and 31 bp overlapping sequences are interspersed throughout the whole genome. The two rRNA genes (lrRNA and srRNA) are 1327 bp and 770 bp in size, with their AT contents of 87.8% and 85.5%, respectively. All tRNAs display typical secondary cloverleaf structures except for tRNASer(AGN) which loses the DHU arm. The 401 bp long AT-rich region contains several features characteristic of the lepidopterans, such as the ATAGA motif followed by a 19 bp poly-T stretch, a microsatellite-like (AT)7element preceded by the ATTTA motif and a 9 bp poly-A stretch. [ABSTRACT FROM AUTHOR]

The mitochondrial genome of Hebomoia glaucippe (Lepidoptera: Pieridae) is a circular molecule of 15,701 bp in length, containing 37 typical mitochondrial genes and an AT-rich region. Its gene arrangement pattern is identical with those of other butterfly species. All protein-coding genes start with ATN start codon except for the cox1 gene, which uses CGA as the initiation codon. A total of 109 bp intergenic spacers and a total of 38 bp overlapping sequences are interspersed throughout the whole genome. The 899-bp long AT-rich region is the second longest among the completely sequenced lepidopteran insects, and contains the motif ATAGA followed by an 19-bp poly-T stretch, two microsatellite-like (AT)10 elements, a duplicated 271-bp repeat element, and two extra tRNALeu(UUR)-like genes. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome (mitogenome) of Melanitis leda (Lepidoptera: Nymphalidae: Satyrinae) is a circular molecule of 15,122 bp in length, containing 37 typical animal mitochondrial genes and 1 control region, known in insects as the AT-rich region. Its gene content and order are identical to all other available butterfly mitogenomes. All protein-coding genes (PCGs) start with a typical ATN initiation codon, except for COI, which is initiated by the CGA codon as observed in other butterfly species. A total of 97 bp of intergenic spacers are interspersed in 11 regions, ranging in size from 1 to 45 bp. The 314-bp-long AT-rich region is the smallest of all the butterfly corresponding regions available and contains some conserved structures similar to those found in other butterfly mitogenomes, including the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (AT)6 element preceded by the ATTTA motif. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of Danaus chrysippus (Lepidoptera: Nymphalidae: Danainae) was determined. The 15,236 bp long genome encodes 13 putative proteins, two ribosomal RNAs, 22 tRNAs and a non-coding AT-rich region. Its gene arrangement pattern is identical to most of other lepidopteran species. All protein-coding genes start with a typical ATN codon with the exception of COI gene which uses CGA as its initial codon; all PCGs terminate in the common stop TAA or TAG, except COI, COII, ND5 and ND4 which use single T as their stop codons. A total of 102 bp intergenic spacers and a total of 33 bp overlapping sequences are interspersed throughout the whole genome. The mitogenome harbors 22 txRNAs as those of most insect species and all tRNA genes evidence the typical clover leaf secondary structures with the exception of tRNAser (AGN) who loses its dihydrouridine (DHU) arm. The lrRNA and srRNA genes are 1339 and 783 bp, with the AT contents of 84.1 and 84.8%, respectively. The non-coding AT-rich region is 418 bp long, and contains the motif ATAGA followed by a 21-bp poly-T stretch and a microsatellite-like (AT)9 element preceded by the ATTTA motif. [ABSTRACT FROM AUTHOR]

The mitochondrial genome of Hybris subjacens (Neuroptera: Ascalaphidae) is a circular molecule of 15,873 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most insect mitogenomes. All PCGs start with a typical ATN codon except for COI and ND1 which use CTT and TTG as their start codon, respectively; all PCGs terminate in the common stop codon TAA or TAG, except for the COI and ND5 which use single T as their stop codons. The non-coding AT-rich region is 1051 bp long, located between rrnS and tRNAlle genes. It contains some structures of repeated motifs and microsatellite-like elements characteristic of the neuropterids. [ABSTRACT FROM AUTHOR]

The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides, the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A. fylloides is 15 301 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a 423 bp A+T-rich region. The gene content, orientation and order are identical to the majority of other lepidopteran insects. Phylogenetic reconstruction was conducted using the concatenated 13 protein-coding gene (PCG) sequences of 19 available butterfly species covering all the five butterfly families (Papilionidae, Nymphalidae, Peridae, Lycaenidae and Riodinidae). Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae, which was standing as the sister of Nymphalidae. In addition, we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon., The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides , the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A. fylloides is 15 301 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a 423 bp A+T-rich region. The gene content, orientation and order are identical to the majority of other lepidopteran insects. Phylogenetic reconstruction was conducted using the concatenated 13 protein-coding gene (PCG) sequences of 19 available butterfly species covering all the five butterfly families (Papilionidae, Nymphalidae, Peridae, Lycaenidae and Riodinidae). Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae, which was standing as the sister of Nymphalidae. In addition, we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon.

In the present study, we report the first complete mitochondrial genome (mitogenome) of the Painted Jezebel, Delias hyparete. The mitogenome of Delias hyparete is 15 186 bp in length, and has typical sets of 37 genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding A+T-rich region. All protein-coding genes are initiated by ATN codons, except for COI, which is tentatively designated by the CGA codon, as observed in other butterfly species. A total of 10 PCGs harbored the complete termination codon TAA or TAG, while the COI, COII and ND5 genes ended at a single T residue. All 22 tRNA genes show typical clover structures, with the exception of the tRNA(Ser(AGN)) which lacks the dihydrouridine (DHU) stem and is instead replaced by a simple loop. Thirteen intergenic spacers totaling 153 bp, and 13 overlapping regions totaling 46 bp are scattered throughout the whole genome. The 377 bp long of D. hyparete A+T-rich region is not comprised of large repetitive sequences, but harbors several features characteristic of the lepidopteran insects, including the motif ATAGA followed by an 18 bp poly-T stretch, a microsatellite-like (AT)(5) element preceded by the ATTTA motif, an 10 bp polyA-like stretch (AAAAATAAAA) present immediately upstream tRNA(Met).

The complete mitochondrial genome of the Parathyma sulpitia (Lepidoptera, Nymphalidae, Limenitidinae) was determined. The entire mitochondrial DNA (mtDNA) molecule was 15 268 bp in size. Its gene content and organization were the same as those of other lepidopteran species, except for the presence of the 121 bp long intergenic spacer between trnS1(AGN) and trnE. The 13 protein-coding genes (PCGs) started with the typical ATN codon, with the exception of the cox1 gene that used CGA as its initial codon. In addition, all protein-coding genes terminated at the common stop codon TAA, except the nad4 gene which used a single T as its terminating codon. All 22 tRNA genes possessed the typical clover leaf secondary structure except for trnS1(AGN), which had a simple loop with the absence of the DHU stem. Excluding the A+T-rich region, the mtDNA genome of P. sulpitia harbored 11 intergenic spacers, the longest of which was 121 bp long with the highest A+T content (100%), located between trnS1(AGN) and trnE. As in other lepidopteran species, there was an 18-bp poly-T stretch at the 3'-end of the A+T-rich region, and there were a few short microsatellite-like repeat regions without conspicuous macro-repeats in the A+T-rich region. The phylogenetic analyses of the published complete mt genomes from nine Nymphalidae species were conducted using the concatenated sequences of 13 PCGs with maximum likelihood and Bayesian inference methods. The results indicated that Limenitidinae was a sister to the Heliconiinae among the main Nymphalidae lineages in this study, strongly supporting the results of previous molecular data, while contradicting speculations based on morphological characters.

The complete mitochondrial genome of Apatura ilia (GenBank accession no. JF437925) was determined as a circular DNA molecule of 15 242 bp, with common genes of 13 putative proteins, 2 rRNAs, and 22 tRNAs and of the same gene arrangement as in other sequenced lepidopterans. All protein-coding genes had the typical start codon ATN, except for the COI's using CGA as its start codon as previously demonstrated in other lepidopteran species. The comparison of the nucleotide sequences of the A. ilia mitogenome with ten other Nymphalidae species showed nearly identical gene orientation and arrangement, with only a few alterations in non-coding fragments. The nucleotide composition and codon frequency all fell into the range estimated for the order Lepidoptera. The A. ilia mitochondrial genome had the canonical set of 22 tRNA genes folded in the typical cloverleaf structure, with an unique exception of tRNA(Ser) (AGN). The mitochondrial genes from A. ilia were overlapped in a total of 33 bp at 9 locations, as well as interleaved with a total of 155 bp intergenic spacers, spread over 12 regions with the size ranging from 1 to 49 bp. Furthermore, the spacer between ND6 and Cyt b harbored a microsatellite-like repeat (TA)(23) not found in other completely sequenced nymphalid genomes. The 403 bp AT-rich region harbored two conserved motifs (ATAGA, ATTTA), a 21 bp polyT stretch, a 10 bp poly-A region, along with two microsatellite-like repeats ( (TA)(10) and (TA)(7)), as detected in other nymphalid butterflies.

We investigated the complete mitochondrial genome (mitogenome) of Argyreus hyperbius. The 15156 bp long genome harbored the gene content (13 protein coding genes, 22 tRNA genes, 2 rRNA genes and an A+T-rich region) and the gene arrangement was identical to all known lepidopteran mitogenomes. Mitogenome sequence nucleotide organization and codon usage analyses showed that the genome had a strong A+T bias, accounting for A+T content of 80.8%, with a small negative AT skew (-0.019). Eleven intergenic spacers totaling 96 bp, and 14 overlapping regions totaling 34 bp were scattered throughout the whole genome. As has been observed in other lepidopteran species, 12 of the 13 protein-coding genes (PCGs) were initiated by ATN codons, while the COI gene was tentatively designated by the CGA codon. A total of 11 PCGs harbored the complete termination codon TAA, while the COI and COII genes ended at a single T residue. All of the 22 tRNA genes showed typical clover structures except that the tRNA(Ser(AGN)) lacks the dihydrouridine (DHU) stem which is replaced by a simple loop. The intergenic spacer sequence between the tRNA(Ser(AGN)) and ND1 also contained the ATACTAA motif, which is conserved in all other lepidopterans as well. Additionally, the 349 bp A+T-rich region was not comprised of large tandem repetitive sequences, but harbored a few structures common to other lepidopteran insects, such as the motif ATAGA followed by a 20 bp poly-T stretch, a microsatellite-like (AT)(9) element preceded by the ATTTA motif, and a 5 bp poly-A site present immediately upstream of tRNA(Met). The mitochondrial genomic sequence features found in this study not only contribute to genetic diversity information of the group, but also are useful in future studies of the endangered nymphalid butterfly in population genetic dynamics, species conservation, phylogeography and evolution.