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The African leaf butterfly Kallimoides rumia Doubleday, 1849 (Nymphalidae), lives in the understory of Afrotropical primary forests. Genome skimming with Illumina sequencing of K. rumia permitted assembly of a complete circular mitogenome of 15,234 bp consisting of 80.9% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region. Kallimoides rumia COX1 features an atypical start codon (CGA). Genes ATP6, COX1, COX2, ND2, ND4 and ND5 feature incomplete stop codons, completed by adding 3’ A residues to the mRNA. Phylogenetic reconstruction places K. rumia as a distinct lineage, not closely related to Kallima, consistent with previous phylogenetic hypotheses.

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.

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.

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.

In this study, high-throughput Illumina sequencing was employed to assemble the complete mitochondrial genome of the Meiren yak (Bos grunniens), a local yak breed from Gansu Province, China. The mitochondrial genome is 16,321 bp long with an A + T-biased nucleotide composition and harbors 13 protein-coding, 22 Trna, and 2 rRNA genes, and a noncoding control region. The mitogenomic organization and codon usage are highly similar to those of previously published congeneric mitochondrial genomes. Bayesian phylogenetic analysis indicates that Meiren yak is most closely related to nine other yak breeds (incl. Datong, Huanhu, Pali, Pamir, Polled, Qilian, Seron, Sunan, and Tianjun yaks).

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.

In this study we report the first complete and annotated mitochondrial genome of the Mexican blind brotula, Typhlias pearsei, a troglobitic cavefish endemic to the Yucatán peninsula karst aquifer in southeastern Mexico. Genomic sequencing was accomplished via next generation sequencing (NGS). The resulting mitogenome is 16,813 bp long and, as in most vertebrates, consists of a total of 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs) and two non-coding regions (control region and origin of the light strand replication). Other than a rearrangement in the position of two tRNAs (shuffling between tRNA-Ile and tRNA-Gln), the mitogenome of T. pearsei exhibits a genomic composition and organization similar to that of most teleost mitogenomes. Besides offering this valuable genomic resource for future studies, the resulting mitogenome was used in a comparative context to test the current higher-level taxonomy of ophidiiform fishes and to examine the phylogenetic position of T. pearsei among viviparous brotulas. Our phylogenetic results confirm those from the most comprehensive molecular phylogenetic study of the group. [ABSTRACT FROM AUTHOR]

Semblis atrata is one of three Semblis species distributed in clean brooks and streams in northern Eurasia. Genomic DNA of an S. atrata sample was extracted and sequenced for assembly and annotation of its complete mitogenome. The complete mitochondrial genome of S. atrata was 14,909 bp in length and consisted of 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The S. atrata COX1 gene features a CGA start codon, and COX1, COX2, ND1, and ND5 exhibit incomplete stop codons that are presumed to be completed by the addition of 3' A residues to the mRNA. The nucleotide composition was highly AT biased, accounting for 77.71% of the whole mitogenome. Phylogenetic analysis placed Semblis as sister to Eubasilissa. The complete mitochondrial genome will be helpful for further studies on the population genetics of this species and phylogenetic analyses of Trichoptera. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the banded cusk-eel, Raneya brasilensis (Kaup, 1856), was obtained using next-generation sequencing approaches. The genome sequence was 16,881 bp and exhibited a novel gene order for a vertebrate. Specifically, the WANCY and the nd6 – D-loop regions were re-ordered, supporting the hypothesis that these two regions are hotspots for gene rearrangements in Actinopterygii. Phylogenetic reconstructions confirmed that R. brasiliensis is nested within Ophidiiformes. Mitochondrial genomes are required from additional ophidiins to determine whether the gene rearrangements that we observed are specific to the genus Raneya or to the subfamily Ophidiinae.

In this study, we test and corroborate the phylogenetic position of Heterosyphus within Helictopleurus using mitogenomes and nuclear loci. Our recent samplings revealed that males of the former Heterosyphus sicardi Paulian, 1975 (today under Helictopleurus d'Orbigny, 1915) have extraordinary bilateral clypeal horns which are exclusive within the genus. We provide a taxonomic review of the fungicola species group of Helictopleurus and discuss the systematic position of H. sicardi within the group. The male phenotype of H. sicardi is described and photographs of the body and genitalia of the members of the fungicola group are given, as well as a diagnostic key to species of the group. Helictopleurus fungicola peyrierasi is considered to be a distinct species within the genus (H. peyrierasi stat. rest.). Helictopleurus pluristriatus d'Orbigny, 1915 syn. nov. is established as a junior synonym of H. fungicola (Fairmaire, 1899). [ABSTRACT FROM AUTHOR]

High morphological plasticity in populations of brine shrimp subjected to different environmental conditions, mainly salinity, hindered for centuries the identification of the taxonomic entities encompassed within Artemia. In addition, the mismatch between molecular and morphological evolution rates complicates the characterization of evolutionary lineages, generating taxonomic problems. Here, we propose a phylogenetic hypothesis for Artemia based on two new complete mitogenomes, and determine levels of congruence in the definition of evolutionary units using nuclear and mtDNA data. We used a fossil of Artemia to calibrate the molecular clock and discuss divergence times within the genus. The hypothesis proposed herein suggests a more recent time frame for lineage splitting than previously considered. Phylogeographic analyses were performed using GenBank available mitochondrial and nuclear markers. Evidence of gen e flow, identified through discordances between nuclear and mtDNA markers, was used to reconsider the specific status of some taxa. As a result, we consider Artemia to be represented by five evolutionary units: Southern Cone, Mediterranean--South African, New World, Western Asian, and Eastern Asian Lineages. After an exhaustive bibliographical revision, unavailable names for nomenclatural purposes were discarded. The remaining available names have been assigned to their respective evolutionary lineage. The proper names for the evolutionary units in which brine shrimps are structured remain as follows: Artemia persimilis Piccinelli & Prosdocimi, 1968 for the Southern Cone Lineage, Artemia salina (Linnaeus, 1758) for the Mediterranean-SouthAfrican Lineage, Artemia urmiana Günther, 1899 for the Western Asian Lineage, and Artemia sinica Cai, 1989 for the Eastern Asian Lineage. The name Artemia monica Verrill, 1869 has nomenclatural priority over A. franciscana Kellogg, 1906 for naming the New World Lineage. New synonymies are proposed for A. salina (= C. dybowskii Grochowski, 1896 n. syn., and A. tunisiana Bowen & Sterling, 1978 n. syn.), A. monica (= A. franciscana Kellogg, 1906 n. syn., and A. salina var. pacifica Sars, 1904 n. syn.); A. urmiana (= B. milhausenii Fischer de Waldheim, 1834 n. syn., A. koeppeniana Fischer, 1851 n. syn., A. proxima King, 1855 n. syn., A. s. var. biloba Entz, 1886 n. syn., A. s. var. furcata Entz, 1886 n. syn., A. asiatica Walter, 1887 n. syn., A. parthenogenetica Bowen & Sterling, 1978 n. syn., A. ebinurica Qian & Wang, 1992 n. syn., A. murae Naganawa, 2017 n. syn., and A. frameshifta Naganawa & Mura, 2017 n. syn.). Internal deep nuclear structuring within the A. monica and A. salina clades, might suggest the existence of additional evolutionary units within these taxa. [ABSTRACT FROM AUTHOR]

The mitogenome of the species belonging to the Papilionodea (Lepidoptera) is a double stranded circular molecule containing the 37 genes shared by Metazoa. Eight mitochondrial gene orders are known in the Papilionoidea. MIQGO is the plesiomorphic gene order for this superfamily, while other mitochondrial arrangements have a very limited distribution. 2S1GO gene order is an exception and is present in several Lycaenidae and one species of Hesperiidae. We studied the macrostructural changes generating the gene orders of butterflies by analysing a large data set (611 taxa) containing 5 new mitochondrial sequences/assemblies and 87 de novo annotated mitogenomes. Our analysis supports a possible origin of the intergenic spacer trnQ-nad2, characterising MIQGO, from trnM. We showed that the homoplasious gene order IMQGO, shared by butterflies, species of ants, beetles and aphids, evolved through different transformational pathways. We identify a complicated evolutionary scenario for 2S1GO in Lycaenidae, characterised by multiple events of duplication/loss and change in anticodon of trnS1. We show that the gene orders ES1GO and S1NGO originated through a tandem duplication random loss mechanism. We describe two novel gene orders. Ampittia subvittatus (Hesperiidae) exhibits the gene order 2FFGO, characterised by two copies of trnF, one located in the canonical position and a second placed in the opposite strand between trnR and trnN. Bhutanitis thaidina (Papilionidae) exhibits the gene order 4QGO, characterised by the quadruplication of trnQ.

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. [ABSTRACT FROM AUTHOR]

The Fusarium fujikuroi species complex (FFSC) and F. oxysporum species complex (FOSC) are two related groups of plant pathogens causing a wide diversity of diseases in agricultural crops world wide. The aims of this study are (1) to clarify the phylogeny of the FFSC, (2) to identify potential deviation from tree-like evolution, (3) to explore the value of using mitogenomes for these kinds of analyses, and (4) to better understand mitogenome evolution. In total, we have sequenced 24 species from the FFSC and a representative set of recently analyzed FOSC strains was chosen, while F. redolens was used as outgroup for the two species complexes. A species tree was constructed based on the concatenated alignment of seven nuclear genes and the mitogenome, which was contrasted to individual gene trees to identify potential conflicts. These comparisons indicated conflicts especially within the previously described African clade of the FFSC. Furthermore, the analysis of the mitogenomes revealed the presence of a variant of the large variable (LV) region in FFSC which was previously only reported for FOSC. The distribution of this variant and the results of sequence comparisons indicate horizontal genetic transfer between members of the two species complexes, most probably through introgression. In addition, a duplication of atp9 was found inside an intron of cob, which suggests that even highly conserved mitochondrial genes can have paralogs. Paralogization in turn may lead to inaccurate single gene phylogenies. In conclusion, mitochondrial genomes provide a robust basis for phylogeny. Comparative phylogenetic analysis indicated that gene flow among and between members of FFSC and FOSC has played an important role in the evolutionary history of these two groups. Since mitogenomes show greater levels of conservation and synteny than nuclear regions, they are more likely to be compatible for recombination than nuclear regions. Therefore, mitogenomes can be used as indicators to detect interspecies gene flow.

We describe the complete mitochondrial genome sequence of the Black Lion Tamarin, an endangered primate species endemic to the Atlantic Rainforest of Brazil. We assembled the Leontopithecus chrysopygus mitogenome, through analysis of 523M base pairs (bp) of short reads produced by next-generation sequencing (NGS) on the Illumina Platform, and investigated the presence of nuclear mitochondrial pseudogenes and heteroplasmic sites. Additionally, we conducted phylogenetic analyses using all complete mitogenomes available for primates until June 2017. The single circular mitogenome of BLT showed organization and arrangement that are typical for other vertebrate species, with a total of 16618 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region (D-loop region). Our full phylogenetic tree is based on the most comprehensive mitogenomic dataset for Callitrichidae species to date, adding new data for the Leontopithecus genus, and discussing previous studies performed on primates. Moreover, the mitochondrial genome reported here consists of a robust mitogenome with 3000X coverage, which certainly will be useful for further phylogenetic and evolutionary analyses of Callitrichidae and higher taxa.

The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215–8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.

Cardiocondyla obscurior is native to Southeast Asia but has become successfully established throughout the tropics and subtropics. Here, its mitochondrial genome was assembled from Illumina sequencing data. The genome is 15,213 bp long with a highly asymmetric nucleotide composition, and harbors the typical set of 37 mitochondrial genes and one noncoding control region. All PCGs are initiated with typical ATN codons and are terminated with TAA, TAG or the incomplete T(aa) codon. The control region has a remarkably high A + T content (90.8%) and harbors a 34-bp-long tandem repeat (TA)17. Phylogenetic analysis suggests that it is closely related to Pristomyrmex punctatus.

The endemic Madagascar banded commodore butterfly Precis andremiaja Boisduval, 1833 (Nymphalidae) inhabits forest margins and disturbed habitats. Genome skimming by Illumina sequencing allowed the assembly of a complete circular mitogenome of 15,239 bp from P. andremiaja consisting of 80.2% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the typical butterfly gene order. Precis andremiaja COX1 has a CGA start codon and COX1, COXII, NAD4 and NAD5 exhibit incomplete stop codons. Phylogenetic reconstruction places P. andremiaja as sister to Hypolimnas bolina within a monophyletic nymphalid tribe Junoniini, which is consistent with previous molecular phylogenetic hypotheses.

The Madagascar mother-of-pearl (Salamis anteva) is a leaf-mimicking butterfly endemic to forests in southern Madagascar. Genome skimming by Illumina sequencing permitted assembly of a complete S. anteva circular mitogenome of 15,201 bp consisting of 80.6% AT nucleotides and with an arrangement of 22 tRNAs, 13 protein-coding genes, two rRNAs and a control region common to all butterflies. The mitogenome includes a COX1 gene with an atypical CGA start codon and four genes exhibiting incomplete stop codons. Phylogenetic reconstruction places S. antvea as sister to Yoma sabina within a monophyletic nymphalid tribe Junoniini. This is consistent with previous molecular phylogenetic hypotheses.

The pale summer sedge caddisfly, Limnephilus hyalinus Hagen, 1861 (Limnephilidae, the Northern Caddisflies), is widespread in North America. Genome skimming by Illumina sequencing allowed assembly of a complete 15,168 bp circular mitogenome from L. hyalinus consisting of 78.0% AT nucleotides, 22 tRNAs, 13 protein-coding genes, two rRNAs and a control region in the ancestral insect gene order. Limnephilus hyalinus COX1 features an atypical CGA start codon while ATP8, NAD1, NAD5, and NAD6 exhibit incomplete stop codons. The mtTERM binding site is conserved between the Trichoptera and the Lepidoptera. Phylogenetic reconstruction reveals a monophyletic Order Trichoptera, Family Limnephilidae, and genus Limnephilus.

Aim: We investigate the spatiotemporal context of the diversification of Allobates, a widespread genus of Amazonian frogs with high species diversity particularly in western Amazonia. We tested if that diversity originated in situ or through repeated dispersals from other Amazonian areas and if this diversification took place during or after the Pebas system, a vast lacustrine system occupying most western Amazonia between 23 and 10 million years ago (Mya). Location: Amazonia. Taxon: Allobates (Anura: Aromobatidae). Methods: We gathered a spatially and taxonomically extensive sampling of mitochondrial DNA sequences from 932 Allobates specimens to delimit Operational Taxonomic Units (OTUs). Complete mitogenomes of these OTUs were assembled to reconstruct a time‐calibrated phylogeny used to infer the historical and spatial origin of the Amazonian Allobates lineages. Results: Phylogenetic analyses and ancestral area reconstruction suggested that most of the western Amazonian lineages resulted from in situ diversification and that these events occurred between the inferred origin of the genus (25 Mya) and 10 Mya, with a possible peak between 14 and 10 Mya. Dispersal among areas mostly occurred from western Amazonia towards the Brazilian and the Guiana Shields. Closely related Allobates OTUs display an allopatric pattern of distribution, matching interfluves delimited by modern Amazonian rivers. Main Conclusions: In western Amazonia, diversification of Allobates appears to have been simultaneous with the last stages of the Pebas system (14–10 Mya). Subsequently (within the last 10 Mya), modern Amazonian river courses shaped the distribution pattern of Allobates species and possibly promoted allopatric speciation. [ABSTRACT FROM AUTHOR]

This study presents the first complete mitochondrial genome (mitogenome) of Caecobarbus geertsii , the Congo blind barb, a cave-dwelling, CITES-protected, cyprinid fish endemic to the Lower Congo basin (DRC). The length of the circular mitogenome is 16,565 base pairs. The 13 protein coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes are similar in position and direction to those of other members of the family Cyprinidae. Phylogenetic analyses including 28 complete mitogenomes from representatives of the subfamily Smiliogastrinae (Cyprinidae), showed that Caecobarbus was nested within a clade including representatives of the genus Enteromius. The data presented in this study provide information on the molecular identification and classification of this threatened species. The results further suggest the need for a taxonomic revision of the genus Enteromius. [ABSTRACT FROM AUTHOR]

Copepods are important ecologically and represent a large amount of aquatic biomass in both freshwater and marine systems. Despite this, the taxonomy of copepods and other meiofauna is not well understood, hampered by tiny sizes, cryptic taxa, intraspecific polymorphisms and total specimen destruction where DNA methods are employed. In this article we highlight these issues and propose a more up-to-date approach for dealing with them. Namely, we recommend non-destructive DNA extraction methods, coupled with high-throughput sequencing (HTS). Whilst DNA yields may be low, they should still be sufficient for HTS library preparation and DNA sequencing. At the same time morphological specimens can be preserved and the crucial link between morphology and DNA sequence is maintained. This is critical for an integrative taxonomy and a fuller understanding of biodiversity patterns as well as evolutionary processes in meiofauna. [ABSTRACT FROM AUTHOR]

In this study, we sequenced two complete mitochondrial genomes of Amblyomma ovale, a tick of public health importance. Sequencing two distinct individuals, the resulting mitochondrial genomes were 14,756 and 14,760 bp in length and maintained the same gene order previously reported in Amblyomma. These were combined with RNA-seq derived mitochondrial sequences from three additional species, Amblyomma aureolatum, Amblyomma maculatum, and Amblyomma moreliae, to carry out mitogenome comparative and evolutionary analyses against all previously published tick mitochondrial genomes. We described a derivative genome rearrangement that isolates Ixodes from the remaining Ixodidae and consists of both a reverse translocation as well as an event of Tandem Duplication Random Loss. Genetic distance analyses indicated that cox2, nd1, nd5, and 16S are good candidates for future population studies in A. ovale. The phylogenetic analyses corroborated the utility of complete mitochondrial genomes as phylogenetic markers within the group. This study further supplements the genome information available for Amblyomma and facilitates future evolutionary and population genetic studies within the genus. [ABSTRACT FROM AUTHOR]

Ethiopian rats (genus Stenocephalemys) represent a monophyletic group of Ethiopian endemic rodents that diverged in the Ethiopian Highlands during the Pleistocene. Because of the frequent occurrence of socalled reticulate evolution (i.e. repeated hybridization of partially diverged populations), their taxonomy has not been adequately resolved, despite the fact that they belong to the most abundant rodent genus in Ethiopia and are important as pests and carriers of pathogens (e.g. hantaviruses). Here we analysed material for 623 Stenocephalemys specimens using integrative taxonomy composed of genomic analyses (388 nuclear markers and complete mitogenomes), 2D-geometric morphometry of skulls and classical morphometry of external traits. The genus consists of six clearly defined gene pools (= species), characterized by specific morphology, ecology and distribution. Two of them, described here as new species, live in fragmented populations in Afroalpine habitats in the north-western part of the Ethiopian Highlands. We also showed that mitochondrial DNA is not applicable as a universal diagnostic tool for species discrimination in Stenocephalemys, because of multiple cases of mitochondrial introgression. This finding illustrates the utility of the genus as a suitable model for future studies of mito-nuclear coevolution along an elevational gradient. [ABSTRACT FROM AUTHOR]

The Fusarium fujikuroi species complex (FFSC) and F. oxysporum species complex (FOSC) are two related groups of plant pathogens causing a wide diversity of diseases in agricultural crops world wide. The aims of this study are (1) to clarify the phylogeny of the FFSC, (2) to identify potential deviation from tree-like evolution, (3) to explore the value of using mitogenomes for these kinds of analyses, and (4) to better understand mitogenome evolution. In total, we have sequenced 24 species from the FFSC and a representative set of recently analyzed FOSC strains was chosen, while F. redolens was used as outgroup for the two species complexes. A species tree was constructed based on the concatenated alignment of seven nuclear genes and the mitogenome, which was contrasted to individual gene trees to identify potential conflicts. These comparisons indicated conflicts especially within the previously described African clade of the FFSC. Furthermore, the analysis of the mitogenomes revealed the presence of a variant of the large variable (LV) region in FFSC which was previously only reported for FOSC. The distribution of this variant and the results of sequence comparisons indicate horizontal genetic transfer between members of the two species complexes, most probably through introgression. In addition, a duplication of atp9 was found inside an intron of cob , which suggests that even highly conserved mitochondrial genes can have paralogs. Paralogization in turn may lead to inaccurate single gene phylogenies. In conclusion, mitochondrial genomes provide a robust basis for phylogeny. Comparative phylogenetic analysis indicated that gene flow among and between members of FFSC and FOSC has played an important role in the evolutionary history of these two groups. Since mitogenomes show greater levels of conservation and synteny than nuclear regions, they are more likely to be compatible for recombination than nuclear regions. Therefore, mitogenomes can be used as indicators to detect interspecies gene flow. [ABSTRACT FROM AUTHOR]

The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48–3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations. [ABSTRACT FROM AUTHOR]

The olive shells of the genus Amalda comprises readily recognized species of marine neogastropod mollusks found around the world. The New Zealand Amalda fauna has particular notoriety as providing one of the best demonstrations of evolutionary morphological stasis, a prerequisite for punctuated equilibrium theory. An excellent fossil record includes representation of three extant endemic Amalda species used to explore patterns of form change. However, the phylogenetic relationship of the New Zealand Amalda species and the timing of their lineage splitting have not been studied, even though these would provide valuable evidence to test predictions of punctuated equilibrium. Here, we use entire mitogenome and long nuclear rRNA gene cassette data from 11 Amalda species, selected from New Zealand and around the world in light of high rates of endemicity among extant and fossil Amalda. Our inferred phylogenies do not refute the hypothesis that New Zealand Amalda are a natural monophyletic group and therefore an appropriate example of morphological stasis. Furthermore, estimates of the timing of cladogenesis from the molecular data for the New Zealand group are compatible with the fossil record for extant species and consistent with expectations of punctuated equilibrium. [ABSTRACT FROM AUTHOR]

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent‐coverage threshold to filter out false positives, (b) an internal‐standard DNA spike‐in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 =.93, mitogenomes R2 =.95) and a high repeatability across environmental‐sample replicates (barcodes R2 =.94, mitogenomes R2 =.93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species‐specific abundances, and phenology. SPIKEPIPE provides cost‐efficient and reliable quantification of eukaryotic communities. [ABSTRACT FROM AUTHOR]

The mole salamander Ambystoma talpoideum is native to southeastern and central United States, and is listed as a threatened or endangered species by local governments due to anthropogenic disturbance. Here, its mitochondrial genome was characterized from Illumina sequencing reads. The genome is 16,358 bp long with an asymmetric nucleotide composition (34.6% A, 21.1% C, 13.4% G & 30.9% T; light strand), and harbors 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNAs genes and one control region. All PCGs are initiated with the typical ATG codon except for COX1 with GTG as its start codon, and are terminated with TAA, TAG, AGA or the incomplete TA(a)/T(aa) codon. There are seven intergenic spacer and six intergenic overlapping regions with a total length of 254 and 37 bp, respectively. Phylogenetic analysis corroborated the current taxonomic framework of the suborder Salamandroidea, and suggested that A. talpoideum is closely related to its congeners. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The white seabream Diplodus sargus (Linnaeus, 1758) is a species of interest for commercial fisheries throughout its range of distribution and it is also reared using aquaculture techniques. Herein, we present the first complete sequence and annotation of the mitochondrial genome of this species. The D. sargus mitogenome is 16,515 base pairs in length and contains 13 protein-coding genes, 2 rRNA, 22 tRNA, and 2 non-coding regions (D-loop and L-origin). The overall nucleotide composition is: 27.3% A, 28.9% C, 26.8% T, and 17.0% G. Maximum likelihood analyses placed D. sargus as a sister species of Diplodus puntazzo. This study provides valuable information for further studying identification methods and evolutionary relationships of Sparidae species. [ABSTRACT FROM AUTHOR]

Tetrahymena rostrata is a ciliated protist which can parasitize the gray field slug, Deroceras reticulatum. Here, we report the sequence of the mitochondrial genome (mt genome) of a strain of T. rostrata that was isolated from the egg of D. reticulatum. Whole cell genomic DNA was sequenced using Illumina® MiSeq and the mitochondrial DNA sequence reads were extracted and assembled. The resulting 47,235 bp assembly contained rRNAs, tRNAs, and 45 protein coding DNA sequences of which 21 encoded proteins of unknown function. Phylogenetic analysis showed T. rostrata clustered with Tetrahymena thermophila, Tetrahymena pigmentosa, Tetrahymena pyriformis, Tetrahymena paravorax, and Tetrahymena malaccensis.

The complete mitochondrial genome of the true bug (Homoptera) Nysius cymoides (Spinola, 1837) is herein described and used for phylogenetic comparison with other species of Lygaeoidea. The mtDNA has a gene order and other molecular features typically observed in hexapods, and a long A + T-rich region, due to the occurrence of several repeat units. The phylogenetic analyses support the monophyly of all families except Rhyparochromidae. [ABSTRACT FROM AUTHOR]

The rush sedge caddisfly Phryganea cinerea Walker, 1852 (Phryganeidae, the giant casemakers), is a widespread and adaptable North American caddisfly. Genome skimming by Illumina sequencing permitted the assembly of a complete 15,043 bp circular mitogenome from P. cinerea consisting of 78.2% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the ancestral insect gene order. Phryganea cinerea COX1 features an atypical CGA start codon and COX1, NAD1, NAD4, and NAD5 exhibit incomplete stop codons completed by the addition of 3′ A residues to the mRNA. Phylogenetic reconstruction reveals a monophyletic Order Trichoptera and Family Phyrganeidae.

The ‘D. bakoue species complex’ Rafael, 1984 (‘D. montium species group’ Da Lage et al., 2007) comprises seven Afrotropical species. Using complete mitochondrial genome sequences and detailed morphological analysis, we revised the phylogenetic relationships between these species including two new ones. We found the ‘D. bakoue species complex’ to be a junior synonym of the ‘D. seguyi species complex’ Lachaise, 1971 and its seven species polyphyletic. We thus classified the species into three complexes, the ‘D. seguyi species complex’ comprises D. seguyi Smart, 1945, D. malagassya Tsacas & Rafael, 1982, D. curta Chassagnard & Tsacas, 1997 and D. chocolata sp. nov., the new ‘D. tsacasi species complex’ comprises D. tsacasi Bock & Wheeler, 1972 and D. seguyiana Chassagnard & Tsacas, 1997, and the new ‘D. vulcana species complex’ comprises D. vulcana Graber, 1957 and D. mylenae sp. nov. Drosophila bakoue Tsacas & Lachaise, 1974 could not be assigned to any of the defined complexes. The two new species are endemic to Madagascar and we report the presence of D. seguyi and D. curta in Mayotte and Madagascar, respectively. The results hence represent a significant step towards understanding the diversity and evolution of this species group in Africa and the islands of the Western Indian Ocean.

The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the “no budget mitogenomics” approach ideal for comprehensive molecular studies, especially for subsampled taxa.

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).

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.

The complete mitogenome of Anodonta cygnea is 15,613 bp long. This compact, circular molecule contains the set of 37 genes, typical for invertebrate mitogenomes, in the same order and orientation as in maternally inherited genomes of other bivalves from the same subfamily. There are only two unassigned regions longer than 200 bp (266 bp and 274 bp) and no indication of any supranumerary open reading frames.

There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.

The common dentex (Dentex dentex (Linnaeus, 1758)) is an iconic fish in the Mediterranean diet. Due to its commercial and organoleptic importance, this sparid is highly appreciated in European markets and is often subjected to species substitution frauds. Comparative mitogenomics is a suitable approach for identifying new and effective barcode markers. This study aimed to find a molecular tag useful for unequivocally discriminating the sparid species D. dentex. The comparison of the complete mitochondrial DNA (mtDNA) sequences of 16 sparid species allowed us to highlight the potential of the NAD2 gene for direct identification purposes. Common dentex-specific primers were created and successfully evaluated by end-point and real-rime PCR (Polymerase Chain Reaction) for several fish species, achieving amplification only in the D. dentex. The method proposed in this study appears fast, simple, and inexpensive and requires affordable instrumentation. This approach provides unambiguous results for the common dentex authentication without the sequencing step. The presence/absence assay for D. dentex can be executed in a few hours of lab work. Therefore, national authorities responsible for food safety and traceability could apply and make full use of DNA-testing methods for deterring operators from false seafood declarations.

Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from 2 genetic lineages of Phellinus noxius. Gene order is largely collinear, while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high horizontal gene transfer frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes of Phellinus noxius , mitogenomes' intraspecific polymorphisms at protein-coding sequences are extremely low. Phylogeny network based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mitochondrial DNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes. [ABSTRACT FROM AUTHOR]

Sparids have different organoleptic properties that correlate with a wide variety of retail prices in the market. Components of the observed morphology are rarely sufficient for full identification of these fish species, whose authentication requires specialist knowledge. Genetic diversity or variation and their measurements enable molecular methods as one of the most suggested remedies for aliud pro alio frauds. Genetic approaches have the potential for reducing costs and providing correct identification for a large number of market products. Mitochondrial (mt) DNA sequences (16S and 12S ribosome subunits, cytochrome b- CYTB , and cytochrome c oxidase I- COI) have been widely used for fish species identification. Yet, these mtDNA regions perform well for certain species but are less discriminating for others. Here, we report the first study of the whole mtDNA of the perciform fishes of the family Sparidae with the aim to select more efficient barcoding markers for taxonomical discrimination against frauds. For species-level sequence information, we analyzed and compared the whole sequence of thirteen Sparidae mitogenomes, nine publicly available and four recently sequenced ones. In particular, we searched for effective DNA barcode markers for the correct identification of sparid species by looking for interspecific variable regions flanked by conserved sequences for PCR primer design. We found that only four mtDNA genes are devoid of insertions or deletions, which can complicate the process of sequence alignment. Among them, NAD genes show encouraging utility in discriminating closely related sparid species owing to nucleotide sequence variability compared with classical barcodes for species. Discrimination capacity of NAD genes suggests their application as alternative mtDNA tools for the identification of Sparidae fishes. In particular, NAD5 fragments with high interspecific nucleotide sequence divergence were amplified and appear flawless for Sparidae species identification. • We compared the mtDNA of thirteen Sparidae species for barcoding applications. • We searched for variable regions flanked by conserved sequences for PCR primer design. • NAD5 showed high nucleotide variability flanked by a high number of conserved areas. • NAD5 gene may be an alternative and effective barcode marker for Sparids. • New markers could be used for species characterization in seafood products. [ABSTRACT FROM AUTHOR]

The family Picidae is classified in the order Piciformes with 236 recognized species in 35 genera. Phylogenetic relationships within the Piciformes are still unresolved by major cause of plumage convergence. This study presented two new mitogenomes of Picidae, Darjeeling woodpecker (Dendrocopos darjellensis) and Gray-capped woodpecker (Yungipicus canicapillus), with the size of 16,727 and 16,847 bp, respectively. They have the identical gene order: 37 genes, including 13 PCGs, two rRNA genes, 22 tRNA genes, and two control regions. Furthermore, an extra cytosine insertion at position 174 of MT-ND3 was also found in both species. The MT-RNR1 of Y. canicapillus shared 89.0% nucleotide sequence identity and a similar secondary structure with that of D. darjellensis , consisting of 46 helices and three main domains. There is more divergence in the MT-RNR2 secondary structures than those of MT-RNR1 between the two species. We found the highest dN/dS for the MT-ATP8 (0.08326) among Piciformes, while the lowest for the MT-CO1 (0.00802). Our phylogenetic analyses suggested that the subfamily Picumninae is paraphyletic, and D. darjellensis had a closer relationship with D. major than D. leucotos. The findings of the present study will be useful for further investigating the evolutionary relationships within Piciformes. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the banded cusk-eel, Raneya brasilensis (Kaup, 1856), was obtained using next-generation sequencing approaches. The genome sequence was 16,881 bp and exhibited a novel gene order for a vertebrate. Specifically, the WANCY and the nd6 – D-loop regions were re-ordered, supporting the hypothesis that these two regions are hotspots for gene rearrangements in Actinopterygii. Phylogenetic reconstructions confirmed that R. brasiliensis is nested within Ophidiiformes. Mitochondrial genomes are required from additional ophidiins to determine whether the gene rearrangements that we observed are specific to the genus Raneya or to the subfamily Ophidiinae. [ABSTRACT FROM AUTHOR]