Ancient Mitogenomes Suggest Stable Mitochondrial Clades of the Siberian Roe Deer

The roe deer (Capreolus spp.) has been present in China since the early Pleistocene. Despite abundant fossils available for detailed morphological analyses, little is known about the phylogenetic relationships of the fossil individuals to contemporary roe deer. We generated near-complete mitochondrial genomes for four roe deer remains from Northeastern China to explore the genetic connection of the ancient roe deer to the extant populations and to investigate the evolutionary history and population dynamics of this species. Phylogenetic analyses indicated the four ancient samples fall into three out of four different haplogroups of the Siberian roe deer. Haplogroup C, distributed throughout Eurasia, have existed in Northeastern China since at least the Late Pleistocene, while haplogroup A and D, found in the east of Lake Baikal, emerged in Northeastern China after the Mid Holocene. The Bayesian estimation suggested that the first split within the Siberian roe deer occurred approximately 0.34 million years ago (Ma). Moreover, Bayesian skyline plot analyses suggested that the Siberian roe deer had a population increase between 325 and 225 thousand years ago (Kya) and suffered a transient decline between 50 and 18 Kya. This study provides novel insights into the evolutionary history and population dynamics of the roe deer.

The complete mitochondrial genomes of Notiophilus quadripunctatus Dejean, 1826 and Omophron limbatum (Fabricius, 1777): New insights into the mitogenome phylogeny of the Carabidae (Insecta, Coleoptera)

The Carabidae is by far the largest family of the Adephaga, with more than 40,000 described species. Whereas their phylogeny has been extensively studied, convergences and reversals in morphological traits prevent a robust phylogenetic concept so far. In this study, we sequenced the complete mitochondrial genomes of Notiophilus quadripunctatus (Nebriinae) and Omophrom limbatum (Omophroninae) using high-throughput sequencing. Both mitogenomes consisted of a single circular DNA molecule that encoded the typical 13 protein-coding genes, two subunits of mitochondrial RNAs, 22 tRNAs and a putative control region. Our phylogenetic study placed Omophrom limbatum as sister taxon to all other analyzed ground beetle species whereas Notiophilus quadripunctatus was identified as sister to Nebria brevicollis as part of the Nebriinae. The analyses also support the monophyly of the Cicindelidae but place Trachypachus holmbergi (Trachypachidae) within the Carabidae. Nevertheless, almost all carabid subfamilies with more than one analyzed species were identified as monophyla.

Complete Mitochondrial Genomes of Three Nuthatches From the Genus Sitta (Aves: Passeriformes: Sittidae) and Mitogenome-Based Phylogenetic Analysis

Background Nuthatches (genus Sitta) comprise a group of Passeriformes. With the publication of more mitochondrial genome data, there has been considerable focus on the taxonomic status of the nuthatches. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced and analyzed the complete mitochondrial genomes of three species, S. himalayensis, S. nagaensis and S. yunnanensis, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitochondrial genomes of three Sitta species are 16,822-16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister-group of Troglodytidae, and the genus Sitta can be divided into 3 major clades. We demonstrated the phylogenetic relationships within genus Sitta (S. carolinensis + (S. villosa + S. yunnanensis + (S. himalayensis + (S. europaea + S. nagaensis)))).

Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms)

The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.

The Complete Mitochondrial Genomes of Four Species in the Subfamily Limenitidinae (Lepidoptera, Nymphalidae) and a Phylogenetic Analysis

The complete mitogenomes of four species, Neptis thisbe, Neptis obscurior, Athyma zeroca, and Aldania raddei, were sequenced with sizes ranging from 15,172 bp (N. obscurior) to 16,348 bp (Al. raddei). All four mitogenomes display similar nucleotide content and codon usage of protein-coding genes (PCGs). Typical cloverleaf secondary structures are identified in 21 tRNA genes, while trnS1 (AGN) lacks the dihydrouridine (DHC) arm. The gene orientation and arrangement of the four mitogenomes are similar to that of other typical mitogenomes of Lepidoptera. The Ka/Ks ratio of 13 PCGs among 58 Limenitidinae species reveals that cox1 had the slowest evolutionary rate, while atp8 and nad6 exhibited a higher evolutionary rate. The phylogenetic analysis reveals that tribe-levels are well-supported monophyletic groups. Additionally, Maximum Likelihood analysis recovered the relationship (Parthenini + ((Chalingini + (Cymothoini + Neptini)) + (Adoliadini + Limenitidini))). However, a Bayesian analysis based on the same dataset recovered the relationship (Parthenini + (Adoliadini + ((Cymothoini + Neptini) + (Chalingini + Limenitidini)))). These results will offer valuable data for the future study of the phylogenetic relationships for Limenitidinae.

Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of O. xuefengensis, in addition to comparing it against three other complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the O. sinensis and O. xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O. xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O. sinensis. Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.

Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications

Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini.