The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses

The nearly complete mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) was sequenced for its nucleotide sequence of 13,964 bp. The genome has a typical gene order identical to other lepidopteran species. All tRNAs showed same stable canonical clover-leaf structure as those of other insects, except for tRNA^Ser (AGN), in which the dihydrouracil arm (DHU arm) could not form stable stem–loop structure. Anomalous initiation codons have been observed for the cox1 gene, where the ATTACG hexa-nucleotide was believed to be involved in the initiation signaling. Twelve mitochondrial protein-coding gene sequence data were used to infer the phylogenetic relationships among the insect orders. Even though the number of insect orders represented by complete mitochondrial genomes is still limited, several well-established relationships are evident in the phylogenetic analysis of the complete sequences. Monophyly of the Homometabola was not supported in this paper. Phylogenetic analyses of the available species of Bombycoidea, Pyraloidea, Papilionoidea and Tortricidea bolstered the current morphology-based hypothesis that Bombycoidea, Pyraloidea and Papilionoidea are monophyletic (Obtectomera). Bombycoidea (Bombyx mandarina and Antheraea pernyi) and Papilionoidea (P. xuthus and Coreana raphaelis) formed a sister group.     

The complete mitochondrial genome of the butterfly <Emphasis Type="Italic">Apatura metis</Emphasis> (Lepidoptera: Nymphalidae)

As an important pest in the Slender Leaved Willow (Salix alba), Apatura metis is called Freyer’s purple emperor, and its mitochondrial genome is 15,236 bp long. The encoded genes for 22 tRNA genes, two ribosomal RNA (rrnL and rrnS) genes, and 13 protein-coding genes (PCGs), and a control region in the A. metis mitochondria are highly homologous to other lepidopteran species. The mitochondrial genome of A. metis is biased toward a high A + T content (A + T = 80.5%). All protein-coding genes, except for COI begins with the CGA codon as observed in other lepidopterans, start with a typical ATN initiation codon. All tRNAs show the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA ^Ser(AGN) forms a simple loop. The A. metis A + T-rich region contains some conserved structures including a structure combining the motif ‘ATAGA’ and 19 bp poly (T) stretch, which is similar to those found in other lepidopteran mitogenomes. The phylogenetic analyses of lepidopterans based on mitogenomes sequences demonstrate that each of the six superfamilies is monophyletic, and the relationship among them is (((Noctuoidea + (Geometroidea + Bombycoidea)) + Pyraloidea) + Papilionoidea) + Tortricoidea. In Papilionoidea group, our conclusion argues that ((Lycaenidae + Pieridae) + Nymphalidae) + Papilionidae.     

The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga

In this study, we sequenced the mitochondrial (mt) genome of Agrilus mali (Coleoptera: Buprestidae) using next-generation sequencing, and accordingly annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 1458-bp non-coding region. Comparative analysis indicated that the mt genome of A. mali is relatively conserved, with a typical gene content and order identical to those of other coleopterans. However, the newly sequenced mt genome is characterized by a relatively higher A + T content compared with that of other species within the family Buprestidae. Phylogenetic analysis based on Bayesian inference revealed that the evolutionary relationship among the six infraorders of the suborder Polyphaga is (Scirtiformia + (Elateriformia + ((Scarabaeiformia + Staphyliniformia) + (Bostrichiformia + (Cucujiformia))))). However, the topology indicated that the family Buprestidae is a sister group to other Polyphaga infraorders, excluding Scirtiformia as a monophyly, and thus the monophyly of Elateriformia was not supported. This study not only presents the mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles but also examines the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera.     

Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes

We newly sequenced mitochondrial genomes of Spodoptera litura and Cnaphalocrocis medinalis belonging to Lepidoptera to obtain further insight into mitochondrial genome evolution in this group and investigated the influence of optimal strategies on phylogenetic reconstruction of Lepidoptera. Estimation of p-distances of each mitochondrial gene for available taxonomic levels has shown the highest value in ND6, whereas the lowest values in COI and COII at the nucleotide level, suggesting different utility of each gene for different hierarchical group when individual genes are utilized for phylogenetic analysis. Phylogenetic analyses mainly yielded the relationships (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea), evidencing the polyphyly of Macrolepidoptera. The Noctuoidea concordantly recovered the familial relationships (((Arctiidae + Lymantriidae) + Noctuidae) + Notodontidae). The tests of optimality strategies, such as exclusion of third codon positions, inclusion of rRNA and tRNA genes, data partitioning, RY recoding approach, and recoding nucleotides into amino acids suggested that the majority of the strategies did not substantially alter phylogenetic topologies or nodal supports, except for the sister relationship between Lycaenidae and Pieridae only in the amino acid dataset, which was in contrast to the sister relationship between Lycaenidae and Nymphalidae in Papilionoidea in the remaining datasets.     

Complete mitochondrial genomes of Conogethes punctiferalis and C. pinicolalis (Lepidoptera: Crambidae): Genomic comparison and phylogenetic inference in Pyraloidea

Conogethes punctiferalis Guenée, 1854 (Lepidoptera: Crambidae) is a serious polyphagous pest that attacks more than one hundred species of plants. Previously, C. punctiferalis was determined to be composed of two ecotypes; later, Conogethes pinicolalis, was described as a separate species. Due to the prolonged negligence of C. pinicolalis as an independent species, the genetic perspective of the two species is limited. Thus, in this study, 15,332 and 15,336 bp-long complete mitochondrial genome (mitogenome) of the two species were sequenced and compared to each other and to 54 available mitogenomes of Pyraloidea. The comparison of each protein-coding gene (PCG) and rRNA gene of the two congeneric species showed substantial sequence divergence, ranging from 3.13% (ATP8) to 8.3% (COIII), with an average of 5.92%. Phylogenetic analyses using concatenated sequences of 13 PCGs and 2 rRNAs (12,458 bp including gaps), both by maximum likelihood (ML) and Bayesian inference (BI) methods, consistently supported the monophyly of each family (Crambidae and Pyralidae) and subfamily, generally with the highest nodal supports. The subfamilial relationships of ((((Acentropinae + Schoenobiinae) + (Scopariinae + Crambinae)) + Evergestinae) + (Spilomelinae + Pyraustinae)) in Crambidae and the subfamilial relationships of ((((Pyralinae + Epipaschiinae) + Phycitinae) + Galleriilinae)) in Pyralidae were obtained in both analyses. However, nodal supports were substantially low in this study, mainly due to limited taxa.     

The mitochondrial genome contribution to the phylogeny and identification of Metarhizium species and strains

The genus Metarhizium is composed of entomopathogenic fungal biological control agents (BCAs) used for invertebrate pest control. The phylogenetic relationships of species within this genus are still under scrutiny as several cryptic species can be found. In this work, the mitochondrial (mt) genome of Metarhizium brunneum ARSEF 4556 was fully sequenced and a comparative genome analysis was conducted with 7 other available mt genomes, belonging to 5 Metarhizium species: M. anisopliae, M. brunneum, M. robertsii, M. guizhouense and M. majus. Results showed that Metarhizium demonstrates greater conserved stability than other fungal mt genomes. Furthermore, this analysis located 7 diverse regions in both intergenic domains and gene fragments which were ideal for species/strain discrimination. The sequencing of these regions revealed several SNPs among 38 strains tested, 11 of which were uncharacterized. Single gene phylogenies presented variable results which may be used further for intra-species discrimination. Phylogenetic trees based on the concatenation of mt domains and the nuclear ITS1-5.8S-ITS2 region showed discrimination of the species studied and allowed the identification of uncharacterized strains. These were mostly placed within species M. anisopliae and M. brunneum. Five strains clustered together in a clade related to M. brunneum, suggesting that they comprise a cryptic species.     

Characterization of the complete mitochondrial genome of Tryporyza incertulas, in comparison with seven other Pyraloidea moths

The complete 15,223-bp mitochondrial genome (mitogenome) of Tryporyza incertulas (Walker) (Lepidoptera: Pyraloidea: Crambidae) was determined, characterized and compared with seven other species of superfamily Pyraloidea. The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. Compared with other moths of Pyraloidea, the A + T biased (77.0%) of T. incertulas was the lowest. Eleven protein-coding genes (PCGs) utilized the standard ATN, but cox1 used CGA and nad4 used AAT as the initiation codons. Ten protein-coding genes had the common stop codon TAA, except nad3 having TAG as the stop codon, and cox2, nad4 using T, TA as the incomplete stop codons, respectively. All of the tRNA genes had typical cloverleaf secondary structures except trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. There was a spacer between trnQ and nad2, which was common in Lepidoptera moths. A 6-bp motif ‘ATACTA’ between trnS2(UCN) and nad1, a 7-bp motif “AGC(T)CTTA” between trnW and trnC and a 6-bp motif “ATGATA” of overlapping region between atp8 and atp6 were found in Pyraloidea moths. The A + T-rich region contained an ‘ATAGT(A)’-like motif followed by a poly-T stretch. In addition, two potential stem-loop structures, a duplicated 19-bp repeat element, and two microsatellites ‘(TA)₁₂’ and ‘(TA)₉’ were observed in the A + T-rich region of T. incertulas mitogenome. Finally, the phylogenetic relationships of Pyraloidea species were constructed based on amino acid sequences of 13 PCGs of mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. These molecular-based phylogenies supported the morphological classification on relationships within Pyraloidea species.     

Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera

We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A + T composition (79.3%–80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNA^Gln and ND2 (64–87 bp), conserved ATACTAA motif between tRNA^{Ser (UCN)} and ND1, and characteristic features of the A + T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNA^Asn/tRNA^{Ser (AGN)}, instead of the rearrangement tRNA^{Ser (AGN)}/tRNA^Asn, found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea + Noctuoidea + Geometroidea) + Pyraloidea) + Papilionoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae + (Hesperiidae + (Pieridae + ((Lycaenidae + Riodinidae) + Nymphalidae)))) were strongly supported in all analyses (0.98–1 by BI and 96–100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.     

The Complete Mitochondrial Genome of the Beet Webworm,Spoladea recurvalis (Lepidoptera: Crambidae) and Its Phylogenetic Implications

The complete mitochondrial genome (mitogenome) of the beet webworm, Spoladea recurvalis has been sequenced. The circular genome is 15,273 bp in size, encoding 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes and containing a control region with gene order and orientation identical to that of other ditrysian lepidopteran mitogenomes. The nucleotide composition of the mitogenome shows a high A+T content of 80.9%, and the AT skewness is slightly negative (-0.023). All PCGs start with the typical ATN codons, except for COX1, which may start with the CGA codon. Nine of 13 PCGs have the common stop codon TAA; however, COX1, COX2 and ND5 utilize the T nucleotide and ND4 utilizes TA nucleotides as incomplete termination codons. All tRNAs genes are folded into the typical cloverleaf structure of mitochondrial tRNAs, except for the tRNA^Ser(AGY) gene, in which the DHU arm fails to form a stable stem-loop structure. A total of 157 bp intergenic spacers are scattered in 17 regions. The overlapping sequences are 42 bp in total and found in eight different locations. The 329 bp AT-rich region is comprised of non-repetitive sequences, including the motif ATAG, which is followed by a 14 bp poly-T stretch, a (AT₁₁ microsatellite-like repeat, which is adjacent to the motif ATTTA, and a 9 bp poly-A, which is immediately upstream from the tRNA^Met gene. Phylogenetic analysis, based on 13 PCGs and 13 PCGs+2 rRNAs using Bayesian inference and Maximum likelihood methods, show that the classification position of Pyraloidea is inconsistent with the traditional classification. Hesperioidea is placed within the Papilionoidea rather than as a sister group to it. The Pyraloidea is placed within the Macrolepidoptera with other superfamilies instead of the Papilionoidea.     

Comparative Sequence Analysis of the Non-Protein-Coding Mitochondrial DNA of Inbred Rat Strains

The proper function of mammalian mitochondria necessitates a coordinated expression of both nuclear and mitochondrial genes, most likely due to the co-evolution of nuclear and mitochondrial genomes. The non-protein coding regions of mitochondrial DNA (mtDNA) including the D-loop, tRNA and rRNA genes form a major component of this regulated expression unit. Here we present comparative analyses of the non-protein-coding regions from 27 Rattus norvegicus mtDNA sequences. There were two variable positions in 12S rRNA, 20 in 16S rRNA, eight within the tRNA genes and 13 in the D-loop. Only one of the three neutrality tests used demonstrated statistically significant evidence for selection in 16S rRNA and tRNA-Cys. Based on our analyses of conserved sequences, we propose that some of the variable nucleotide positions identified in 16S rRNA and tRNA-Cys, and the D-loop might be important for mitochondrial function and its regulation.     

Characterization of the complete mitochondrial genome of Diplostomum baeri

Despite Diplostomum baeri (Dubois, 1937) being one of the most widely distributed parasites of freshwater fish, there is no complete mitochondrial (mt) genome currently available. The complicated systematics presented by D. baeri has hampered investigations into the species distributions and infective dynamics of the species. Within this study we obtained complete mt genome sequences of D. baeri and assessed its phylogenetic relationship with other species of Digenea. The complete mitochondrial genome of D. baeri is 14,480 bp in length, containing 36 genes in total. The phylogenetic tree resulting from Bayesian inference of concatenated 12 protein coding gene sequences placed D. baeri alongside published mt genomes of Diplostomidae, with the overall taxonomic placement of the genus being a sister lineage of the order Plagiochiida The characterization of further mitochondrial genomes within the family Diplostomidae will help progress phylogenetic and epidemiological investigations as well as providing a framework for the analysis of diagnostic markers to be used in further monitoring of the parasite worldwide.     

The complete mitogenome sequence of the Japanese oak silkmoth, <Emphasis Type="Italic">Antheraea yamamai</Emphasis> (Lepidoptera: Saturniidae)

The 15,338-bp long complete mitochondrial genome (mitogenome) of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae) was determined. This genome has a gene arrangement identical to those of all other sequenced lepidopteran insects, but differs from the most common type, as the result of the movement of tRNA^Met to a position 5′-upstream of tRNA^Ile. No typical start codon of the A. yamamai COI gene is available. Instead, a tetranucleotide, TTAG, which is found at the beginning context of all sequenced lepidopteran insects was tentatively designated as the start codon for A. yamamai COI gene. Three of the 13 protein-coding genes (PCGs) harbor the incomplete termination codon, T or TA. All tRNAs formed stable stem-and-loop structures, with the exception of tRNA^Ser(AGN), the DHU arm of which formed a simple loop as has been observed in many other metazoan mt tRNA^Ser(AGN). The 334-bp long A + T-rich region is noteworthy in that it harbors tRNA-like structures, as has also been seen in the A + T-rich regions of other insect mitogenomes. Phylogenetic analyses of the available species of Bombycoidea, Pyraloidea, and Tortricidea bolstered the current morphology-based hypothesis that Bombycoidea and Pyraloidea are monophyletic (Obtectomera). As has been previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (A. yamamai and Caligula boisduvalii) formed a reciprocal monophyletic group.     

Description of complete mitochondrial genome of the black-veined white,Aporia crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species

The black-veined white, Aporia crataegi (Lepidoptera: Papilionoidea) is nearly extinct in South Korea, although substantial numbers of dried specimens are available. One of the common practices used to rescue such endangered species is to launch a re-introduction program after a proper amount of genetic information is analyzed from donor and donee populations. In this study, we sequenced the complete mitochondrial genome (mitogenome) of A. crataegi to accumulate genetic information for subsequent population studies and to further understand the mitogenome evolution in true butterflies, Papilionoidea. The 15,140-bp long A. crataegi mitogenome has typical sets of 37 genes and is the smallest among the true butterfly species, with overall slightly smaller size genes and regions throughout the genome. The A/T content of the genome (81.3%) is the highest in Pieridae, where A. crataegi belongs, but lower than that of the lycaenid species (81.7%–82.7%). Unlike the diversified or modified usage of an anticodon for tRNA^Ser(AGN), the species of Pieridae including A. crataegi all contain GCT that has been hypothesized as being ancestral for Lepidoptera. A total of 111 bp of non-coding sequences are interspersed in 13 regions, ranging in size from 1–49 bp. Among these sequences, relatively longer ones (≥ 16 bp) all have relatively higher sequence identity to other regions of the genome, suggesting partial duplication of the sequences during A. crataegi evolution.     

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3′ end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA^Glu and tRNA^Phe genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned.     

Assessing genetic variation and population structure of invasive North American beaver (<Emphasis Type="Italic">Castor Canadensis</Emphasis> Kuhl, 1820) in Tierra Del Fuego (Argentina)

The North American beaver (Castor Canadensis) was introduced into Isla Grande de Tierra del Fuego, Argentina in 1946 as a potential source of wild fur. The species showed high growth potential, reaching close to 100,000 individuals from an original founding stock of 25 females and 25 males. Beavers adapted rapidly to their new environment and became invasive, providing an excellent model of successful adaptation of introduced populations to a new habitat. In this study, we used polymorphic mitochondrial (mt) DNA to evaluate genetic variation in the introduced beaver population from Tierra del Fuego. Nucleotide variation in partial sequences of Cytochrome b (500 bp) and 12S rRNA (421 bp) genes and the main non-coding D-loop region (521 bp) were analyzed. Our study allowed to identify 10 different mtDNA lineages in the invasive population, none of them shared among the source populations. The pattern observed is a consequence of cessation of gene flow following expansion of the founding beaver population since the time of its introduction. This approach contributes to the understanding of effects of genetic changes on survival ability and reproductive success of invasive species. It also has important management implications to invasive species.     

Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

Yeasts are leading model organisms for mitochondrial genome studies. The explosion of complete sequence of yeast mitochondrial (mt) genomes revealed a wide diversity of organization and structure between species. Recently, genome-wide polymorphism survey on the mt genome of isolates of a single species, Lachancea kluyveri, was also performed. To compare the mitochondrial genome evolution at two hierarchical levels: within and among closely related species, we focused on five species of the Lachancea genus, which are close relatives of L. kluyveri. Hence, we sequenced the complete mt genome of L. dasiensis, L. nothofagi, L. mirantina, L. fantastica and L. meyersii. The phylogeny of the Lachancea genus was explored using these data. Analysis of intra- and interspecific variability across the whole Lachancea genus led to the same conclusions regarding the mitochondrial genome evolution. These genomes exhibit a similar architecture and are completely syntenic. Nevertheless, genome sizes vary considerably because of the variations of the intergenic regions and the intron content, contributing to mitochondrial genome plasticity. The high variability of the intergenic regions stands in contrast to the high level of similarity of protein sequences. Quantification of the selective constraints clearly revealed that most of the mitochondrial genes are under purifying selection in the whole genus.     

Low genetic diversity in Polish populations of sibling ant species: <Emphasis Type="Italic">Lasius niger</Emphasis> (L.) and <Emphasis Type="Italic">Lasius platythorax</Emphasis> Seifert (Hymenoptera,Formicidae)

We present preliminary data on mitochondrial DNA diversity within and among populations of the ants Lasius niger and Lasius platythorax in Poland. Phylogenetic analysis based on the mitochondrial DNA markers: cytochrome c oxidase subunit I (cox1) and 16S ribosomal RNA (16S rRNA) confirms the species status of L. niger and L. platythorax. Intraspecific variability is low in both species, which might be a result of severe bottlenecks and rapid postglacial expansion into Central Europe.     

Phylogeny,biogeography, and electric signal evolution of Neotropical knifefishes of the genus Gymnotus (Osteichthyes: Gymnotidae)

The Neotropical knifefish genus Gymnotus is the most broadly distributed and the most diverse (34 + species) gymnotiform genus. Its wide range includes both Central and South American drainages, including the Amazon, Orinoco, and La Plata Basins. Like all gymnotiforms, Gymnotus species produce weak electric fields for both navigation and communication, and these fields exhibit interspecific variation in electric waveform characteristics. Both biogeography and electric signal evolution can profitably be analyzed in a phylogenetic context. Here, we present a total evidence phylogeny for 19 Gymnotus species based on data from the mitochondrial cytochrome b and 16S genes (1558 bp), the nuclear RAG2 gene (1223 bp), and 113 morphological characters. Our phylogenetic hypothesis resolves five distinct Gymnotus lineages. In a previous morphology-based analysis, the Central American Gymnotus cylindricus lineage was hypothesized as the sister group to all other Gymnotus species. In our analysis, the G. cylindricus lineage is nested within South American species, and molecular age estimates support a relatively recent origin for the clade in Central America. Phylogenetic optimization of electric signal waveforms indicate that the ancestral state in Gymnotus is a multiphasic (4 + phases of alternating polarity) condition, and independent phase loss has occurred in multiple lineages. Gymnotus is a model group for understanding Neotropical diversification and the evolution of communication at a continental scale.     

Complete nucleotide sequence and organization of the mitogenome of the red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) and comparison with other lepidopteran insects

The 15,389-bp long complete mitogenome of the endangered red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) was determined in this study. The start codon for the COI gene in insects has been extensively discussed, and has long remained a matter of some controversy. Herein, we propose that the CGA (arginine) sequence functions as the start codon for the COI gene in lepidopteran insects, on the basis of complete mitogenome sequences of lepidopteran insects, including P. bremeri, as well as additional sequences of the COI start region from a diverse taxonomic range of lepidopteran species (a total of 53 species from 15 families). In our extensive search for a tRNA-like structure in the A+T-rich region, one tRNA^Trp-like sequence and one tRNA^Leu (UUR)-like sequence were detected in the P. bremeri A+T-rich region, and one or more tRNA-like structures were detected in the A+T-rich region of the majority of other sequenced lepidopteran insects, thereby indicating that such features occur frequently in the lepidopteran mitogenomes. Phylogenetic analysis using the concatenated 13 amino acid sequences and nucleotide sequences of PCGs of the four macrolepidopteran superfamilies together with the Tortricoidea and Pyraloidea resulted in the successful recovery of a monophyly of Papilionoidea and a monophyly of Bombycoidea. However, the Geometroidea were unexpectedly identified as a sister group of the Bombycoidea, rather than the Papilionoidea.     

Complete mitochondrial genomes of three lizard species and the systematic position of the Lacertidae (Squamata)*

Complete mitochondrial (mt) genomes were sequenced from representatives of three lacertid lizards: Podarcis siculus, Podarcis muralis and Phoenicolacerta kulzeri. In all three genomes the arrangement of the 22 tRNAs, the two rRNAs and the 13 protein‐coding genes conforms to the common vertebrate arrangement. The phylogenetic position of Lacertidae within the order Squamata was determined through sequence analyses based on large sections of complete mt genomes. The number of nucleotide sites used for tree construction was 9234 when outgroup taxa were included, and 10 499 when only Squamata were compared. The phylogenetic analyses confirmed the sister group relationship between Lacertidae and Amphisbaenia as previously proposed on the basis of molecular data. Additionally, Bayesian analysis revealed a well supported clade comprising (Gekkonidae (Lacertidae + Amphisbaenia)), which is not in accordance with the traditional morphological view and most of the previous molecular studies. It confirms, however, the close relationship between Gekkonidae and Amphisbaenia as revealed in a recent study based on complete mt genomes from a smaller number of taxa. Intra‐ and intergeneric sequence comparisons of six commonly used marker genes showed rather high levels of divergence within the Lacertidae. In the intrageneric comparison the control region proved to be considerably more conserved than the protein coding genes.