Mitogenome Evolution Research Articles

Divergence history and hydrothermal vent adaptation of decapod crustaceans: A mitogenomic perspective.

Decapod crustaceans, such as alvinocaridid shrimps, bythograeid crabs and galatheid squat lobsters are important fauna in the hydrothermal vents and have well adapted to hydrothermal vent environments. In this study, eighteen mitochondrial genomes (mitogenomes) of hydrothermal vent decapods were used to explore the evolutionary history and their adaptation to the hydrothermal vent habitats. BI and ML algorithms produced consistent phylogeny for Decapoda. The phylogenetic relationship revealed more evolved positions for all the hydrothermal vent groups, indicating they migrated from non-vent environments, instead of the remnants of ancient hydrothermal vent species, which support the extinction/repopulation hypothesis. The divergence time estimation on the Alvinocarididae, Bythograeidae and Galatheoidea nodes are located at 75.20, 56.44 and 47.41–50.43 Ma, respectively, which refers to the Late Cretaceous origin of alvinocaridid shrimps and the Early Tertiary origin of bythograeid crabs and galatheid squat lobsters. These origin stories are thought to associate with the global deep-water anoxic/dysoxic events. Total eleven positively selected sites were detected in the mitochondrial OXPHOS genes of three lineages of hydrothermal vent decapods, suggesting a link between hydrothermal vent adaption and OXPHOS molecular biology in decapods. This study adds to the understanding of the link between mitogenome evolution and ecological adaptation to hydrothermal vent habitats in decapods.

Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina.

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

Mitochondrial‐encoded endonucleases drive recombination of protein‐coding genes in yeast

Mitochondrial recombination in yeast is well recognized, yet the underlying genetic mechanisms are not well understood. Recent progress has suggested that mobile introns in mitochondrial genomes (mitogenomes) can facilitate the recombination of their corresponding intron-containing genes through a mechanism known as intron homing. As many mitochondrial genes lack introns, there is a critical need to determine the extent of recombination and underlying mechanism of intron-lacking genes. This study leverages yeast mitogenomes to address these questions. In Saccharomyces cerevisiae, the 3'-end sequences of at least three intron-lacking mitochondrial genes exhibit elevated nucleotide diversity and recombination hotspots. Each of these 3'-end sequences is immediately adjacent to or even fused as overlapping genes with a stand-alone endonuclease. Our findings suggest that SAEs are responsible for recombination and elevated diversity of adjacent intron-lacking genes. SAEs were also evident to drive recombination of intron-lacking genes in Lachancea kluyveri, a yeast species that diverged from S. cerevisiae more than 100 million years ago. These results suggest SAEs as a common driver in recombination of intron-lacking genes during mitogenome evolution. We postulate that the linkage between intron-lacking gene and its adjacent endonuclease gene is the result of co-evolution.

The conserved mitochondrial genomes of Drosophila mercatorum (Diptera: Drosophilidae) with different reproductive modes and phylogenetic implications

Fruit flies (Drosophilidae: Drosophila) are commonly found in daily life and have long been used as model organisms in biology researches. Drosophila mercatorum is one important member of the Drosophila genus and has been used to study centrosome assembly of cells. In this study, we sequenced and analyzed the mitochondrial genome (mitogenome) of D. mercatorum, finding that it contains the typical structure of 37 genes and a control region. The arrangement of mitochondrial genes is in accordance with that in other Drosophila species, which is considered the ancestral organization of insects' mitogenomes. Phylogenetic analyses were performed based on 23 species of Drosophila. Our results supported two monophyletic subgenera, Drosophila and Sophophora, except for D. willistoni which was presented as an early offshoot of Drosophila. The topology ((D. yakuba + D. erecta) + D. melanogaster) was supported. We further compared the mitogenomes of parthenogenesis and sexual reproduction strains of D. mercatorum. However, only one synonymous mutation in COI gene was identified, indicating mitogenomic evolution is not strongly correlated with the different reproductive modes of this species. Taken together, our results demonstrate that mitogenome is an effective molecular marker that can be further used in phylogenetic studies of Drosophila and other organisms.

Comparative mitogenomic analysis of species in the subfamily Amphinemurinae (Plecoptera: Nemouridae) reveal conserved mitochondrial genome organization

The subfamily Amphinemurinae has five genera in China, with each genus of similar morphology. To gain a better understanding of architecture and evolution of mitogenome in Amphinemurinae, mitogenomes of eight species representing four genera (Amphinemura, Indonemoura, Protonemura and Sphaeronemoura) in the subfamily Amphinemurinae were sequenced, and a comparative mitogenomic analysis of five genera (including a published stonefly genus, Mesonemoura) was carried out. By comparative analysis, we found highly conserved genome organization of ten Amphinemurinae species including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. GC content was the most significant factor in determining codon bias among organisms. The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. We also found some important conserved stem and loop in the cloverleaf structure of tRNAs, and found conserved helices and loops in each domain of the secondary structure of rRNAs. The presence of structural elements in the control region is also discussed. The phylogenetic analyses indicated that within Amphinemurinae, Sphaeronemoura was assigned the sister group of Mesonemoura. Our analyses inferred a relationship within Euholognatha: ((Nemouridae + Notonemouridae) + (Taeniopterygidae + Capniidae) + Scopuridae) + Leuctridae.

Characterization of the complete mitochondrial genome of Zhenhai brown frog Rana zhenhaiensis (Anura: Ranidae)

Rana zhenhaiensis is a species of frog within the family Ranidae. In this study, its complete mitochondrial genome was characterized by high-throughput sequencing technology. It is 19,205 bp long with an overall AT content of 55.2% and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 control region. Besides, a 26-bp-long origin of L-strand replication (OL) is present between tRNA-Asn and tRNA-Cys. Our findings will be useful for the detailed study of mitogenome evolution and the phylogenetic relationships of the genus Rana and related taxa.

Mitochondrial variation in small brown planthoppers linked to multiple traits and probably reflecting a complex evolutionary trajectory.

While it has been proposed in several taxa that the mitochondrial genome is associated with adaptive evolution to different climatic conditions, making links between mitochondrial haplotypes and organismal phenotypes remains a challenge. Mitonuclear discordance occurs in the small brown planthopper (SBPH), Laodelphax striatellus, with one mitochondrial haplogroup (HGI) more common in the cold climate region of China relative to another form (HGII) despite strong nuclear gene flow, providing a promising model to investigate climatic adaptation of mitochondrial genomes. We hypothesized that cold adaptation through HGI may be involved, and considered mitogenome evolution, population genetic analyses, and bioassays to test this hypothesis. In contrast to our hypothesis, chill-coma recovery tests and population genetic tests of selection both pointed to HGII being involved in cold adaptation. Phylogenetic analyses revealed that HGII is nested within HGI, and has three nonsynonymous changes in ND2, ND5 and CYTB in comparison to HGI. These molecular changes likely increased mtDNA copy number, cold tolerance and fecundity of SBPH, particularly through a function-altering amino acid change involving M114T in ND2. Nuclear background also influenced fecundity and chill recovery (i.e., mitonuclear epistasis) and protein modelling indicates possible nuclear interactions for the two nonsynonymous changes in ND2 and CYTB. The high occurrence frequency of HGI in the cold climate region of China remains unexplained, but several possible reasons are discussed. Overall, our study points to a link between mtDNA variation and organismal-level evolution and suggests a possible role of mitonuclear interactions in maintaining mtDNA diversity.

Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species

Japalura flaviceps is a subarboreal species, which is endemically distributed in China. Here, we determined the complete mitogenome of J. flaviceps. This mitogenome was a typical circular molecule of 17,140 bp in size, containing 13 protein-coding genes, 22 transfer-RNA-coding genes, two ribosomal-RNA-coding genes, and one control region. Our phylogenetic result using 15 genes divided all Agamidae lizards into six subfamilies and showed (((((Agaminae, Draconinae), Amphibolurinae), Hydrosaurinae), Uromastycinae), Leiolepinae), which was different from the previous studies. J. flaviceps had a closer relationship to Pseudocalotes species than Acanthosaura species, and they formed a well-supported lineage of Draconinae subfamily. There were nine mitochondrial gene rearrangement types among the 27 Agamidae species, and six of them were found in the Agaminae group. The trnP gene of J. flaviceps mitogenome was encoded on the heavy strand instead of its typical light strand position, providing an example of gene inversion in vertebrate mitogenomes. J. flaviceps shared the same gene arrangement type (inverted trnP gene) with other Draconinae species, strongly implying a single occurrence of the trnP inversion in the ancestral draconine lineage. Our study helps to understand mitogenome evolution and phylogenetic relationship of Agamidae species.

Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

BackgroundCosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of eucalyptus in China) in approximately 17 genera. However, very limited information of Cosmoscartini is available except for some scattered taxonomic studies. Even less is known about its phylogenetic relationship, especially among closely related genera or species. In this study, the detailed comparative genomic and phylogenetic analyses were performed on nine newly sequenced mitochondrial genomes (mitogenomes) of Cosmoscartini, with the purpose of exploring the taxonomic status of the previously defined genus Okiscarta and some closely related species within the genus Cosmoscarta.ResultsMitogenomes of Cosmoscartini display similar genomic characters in terms of gene arrangement, nucleotide composition, codon usage and overlapping regions. However, there are also many differences in intergenic spacers, mismatches of tRNAs, and the control region. Additionally, the secondary structures of rRNAs within Cercopidae are inferred for the first time.Based on comparative genomic (especially for the substitution pattern of tRNA secondary structure) and phylogenetic analyses, the representative species of Okiscarta uchidae possesses similar structures with other Cosmoscarta species and is placed consistently in Cosmoscarta. Although Cosmoscarta bimacula is difficult to be distinguished from Cosmoscarta bispecularis by traditional morphological methods, evidence from mitogenomes highly support the relationships of (C. bimacula + Cosmoscarta rubroscutellata) + (C. bispecularis + Cosmoscarta sp.).ConclusionsThis study presents mitogenomes of nine Cosmoscartini species and represents the first detailed comparative genomic and phylogenetic analyses within Cercopidae. It is indicated that knowledge of mitogenomes can be effectively used to resolve phylogenetic relationships at low taxonomic levels. Sequencing more mitogenomes at various taxonomic levels will also improve our understanding of mitogenomic evolution and phylogeny in Cercopidae.

Mitochondrial genome of the garfish Hyporhamphus quoyi (Beloniformes: Hemiramphidae) and phylogenetic relationships within Beloniformes based on whole mitogenomes.

Mitochondrial DNA (mtDNA) can provide genome-level information (e.g. mitochondrial genome structure, phylogenetic relationships and codon usage) for analyzing molecular phylogeny and evolution of teleostean species. The species in the order Beloniformes have commercial importance in recreational fisheries. In order to further clarify the phylogenetic relationship of these important species, we determined the complete mitochondrial genome (mitogenome) of garfish Hyporhamphus quoyi of Hemiramphidae within Beloniformes. The mitogenome was 16,524 bp long and was typical of other teleosts mitogenomes in size and content. Thirteen PCGs started with the typical ATG codon (with exception of the cytochrome coxidase subunit 1 (cox1) gene with GTG). All tRNA sequences could be folded into expected cloverleaf secondary structures except for tRNASer (AGN) which lost a dihydrouracil (DHU) stem. The control region was 866 bp in length, which contained some conserved sequence blocks (CSBs) common to Beloniformes. The phylogenetic relationship between 26 fish Beloniformes species was analyzed based on the complete nucleotide and amino acid sequences of 13 PCGs by two different inference methods (Maximum Likelihood and Bayesian Inference). Phylogenetic analyses revealed Hemiramphidae as the sister group to Exocoetidae and it is a paraphyletic grouping. Our results may provide useful information on mitogenome evolution of teleostean species.

The mitochondrial genome of Greenidea psidii van der Goot (Hemiptera: Aphididae: Greenideinae) and comparisons with other Aphididae aphids

The complete mitochondrial genome of Greenidea psidii was sequenced and compared with the genomes of other aphid species. The G. psidii mitogenome is 16,202 bp long with an A + T content of 85.4%, comprising 37 genes arranged in the same order as the inferred insect ancestral arrangement, a control region and a special repeat region between trnE and trnF. G. psidii is the first representative possessing such a repeat region from the subfamily Greenideinae. These repeat motifs found in Aphidinae, Eriosomatinae and Greenideinae are species-specific, differing in nucleotide composition, length and copy number across different species. All reported complete aphid mitogenomes are A- and C-skewed in the whole genomes and show opposite skewness for C and G between the majority and minority strands. The ratios of nonsynonymous to synonymous substitution rates indicated that the evolution of the aphid mitogenomes has been dominated by purifying selection. Based on whole mitogenome sequences, the phylogenetic relationships among all aphid species with complete mitogenomes were investigated. G. psidii was robustly clustered with Cervaphis quercus, confirming its affiliation with the subfamily Greenideinae.

Characterization and comparison of the mitochondrial genomes from two Lyophyllum fungal species and insights into phylogeny of Agaricomycetes

Lyophyllum decastes and Lyophyllum shimeji are the two primary species within the L. decastes complex, and they differ considerably in their nutritional lifestyles and preferred growth environments. However, differences in their mitogenomes have not yet been investigated. In this study, the mitogenomes of the two species were sequenced by next-generation sequencing technology, successfully assembled, and compared. The two mitogenomes of L. decastes and L. shimeji comprised circular DNA molecules of sizes 50,643 bp and 73,678 bp, respectively. The lengths and base compositions of their core protein coding genes (PCGs) and tRNA genes varied considerably between the two mitogenomes. Further, gene collinearity analysis indicated a large-scale gene rearrangement between the two mitogenomes. Of the 15 core PCGs, the genetic distance of the atp9 gene was the smallest between the two species, indicating that this gene was highly conserved in the two Lyophyllum species. Phylogenetic analysis based on a combined mitochondrial gene dataset resulted in a well-supported topology, wherein the two Lyophyllum species were most closely related to Tricholoma matsutake. This study represents the first report of mitogenomes for the Lyophyllum genus. As such, the results will provide a basis for understanding the differentiation and evolution of mitogenomes in the Lyophyllum genus.

Comparative Mitogenomic Analysis of Forensically Important Sarcophagid Flies (Diptera: Sarcophagidae) and Implications of Species Identification

The flesh flies (Diptera: Sarcophagidae) are significant in forensic investigations. The mitochondrial genome (mitogeome) has been widely used as genetic markers for phylogenetic analysis and species identification. To further understand the mitogenome-level features in Sarcophagidae, the complete mitogenome of Sarcophaga formosensis (Kirneret Lopes, 1961) (Diptera: Sarcophagidae) and Sarcophaga misera (Walker, 1849) (Diptera: Sarcophagidae) was firstly sequenced, annotated, and compared with other 13 Sarcophagidae species. The result indicated that the gene arrangement, gene content, base composition, and codon usage were conserved in the ancestral arthropod. Evolutionary rate of the mitogenome fragments revealed that the nonsynonymous and synonymous substitution rates (Ka and Ks) ratio was less than 1.00, indicating these variable sites under strong purifying selection. Almost all transfer RNA genes (tRNAs) have typical clover-leaf structures within these sarcophagid mitogenomes, except tRNA-Ser (AGN) is lack of the dihydrouridine arm. This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the Sarcophagidae. Phylogenetic analyses containing the interspecific distances from different regions in these species provided us new insights into the application of these effective genetic markers for species identification of flesh flies.

Comparative analysis of mitochondrial genomes of the superfamily Grylloidea (Insecta, Orthoptera) reveals phylogenetic distribution of gene rearrangements

To further characterize mitochondrial genome (mitogenome) features of the superfamily Grylloidea (Insecta, Orthoptera), mitogenomes of Cacoplistes rogenhoferi and Meloimorpha japonica representing the family Mogoplistidae and three Ornebius species of Phalangopsidae were sequenced. A repeat-containing control region (CR) and 37 genes were present in these mitogenomes. Unusual start codons (TCG, CCG, and CTG) of cox1 and, in Ornebius, a partial stop codon (T) of nad1 followed by a 15–17-bp intergenic spacer were proposed based on transcript information and sequence alignments. The mitogenome-based phylogenetic trees suggest strongly the familial relationships as (((Phalangopsidae + Gryllidae) + Trigonidiidae) + Mogoplistidae). The exclusive occurrence of the trnE-trnS1-trnN rearrangement in Phalangopsidae, Gryllidae, and Trigonidiidae is suggestive of its appearance in the common ancestor of these families after the separation of Mogoplistidae. The trnV transposition in O. bimaculatus and formerly sequenced Trigonidium sjostedti (Trigonidiidae) indicates a potential consequence of parallel evolution. This study offers novel insights into mitogenome evolution, especially gene rearrangements, of Grylloidea.

Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates.

There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitogenome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species that distribute across different climates. We sequenced 26 complete mitogenomes of Tetranychus truncates, which occurs in both warm and cold regions, and nine complete mitogenomes of Tetranychus pueraricola, which is restricted to warm regions. Patterns of evolution in the two species' mitogenomes were compared through a series of dN /dS methods and physicochemical profiles of amino acid replacements. We found that: (1) the mitogenomes of both species were under widespread purifying selection; (2) elevated directional adaptive selection was observed in the T.truncatus mitogenome, perhaps linked to the cold climates adaptation of T.truncatus; and (3) the strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation.

Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica 'JinhuaiJ2'.

Sophora japonica L. (Faboideae, Leguminosae) is an important traditional Chinese herb with a long history of cultivation. Its flower buds and fruits contain abundant flavonoids, and therefore, the plants are cultivated for the industrial extraction of rutin. Here, we determined the complete nucleotide sequence of the mitochondrial genome of S. japonica ‘JinhuaiJ2’, the most widely planted variety in Guangxi region of China. The total length of the mtDNA sequence is 484,916 bp, with a GC content of 45.4%. Sophora japonica mtDNA harbors 32 known protein-coding genes, 17 tRNA genes, and three rRNA genes with 17 cis-spliced and five trans-spliced introns disrupting eight protein-coding genes. The gene coding and intron regions, and intergenic spacers account for 7.5%, 5.8% and 86.7% of the genome, respectively. The gene profile of S. japonica mitogenome differs from that of the other Faboideae species by only one or two gene gains or losses. Four of the 17 cis-spliced introns showed distinct length variations in the Faboideae, which could be attributed to the homologous recombination of the short repeats measuring a few bases located precisely at the edges of the putative deletions. This reflects the importance of small repeats in the sequence evolution in Faboideae mitogenomes. Repeated sequences of S. japonica mitogenome are mainly composed of small repeats, with only 20 medium-sized repeats, and one large repeat, adding up to 4% of its mitogenome length. Among the 25 pseudogene fragments detected in the intergenic spacer regions, the two largest ones and their corresponding functional gene copies located in two different sets of medium-sized repeats, point to their origins from homologous recombinations. As we further observed the recombined reads associated with the longest repeats of 2,160 bp with the PacBio long read data set of just 15 × in depth, repeat mediated homologous recombinations may play important role in the mitogenomic evolution of S. japonica. Our study provides insightful knowledge to the genetic background of this important herb species and the mitogenomic evolution in the Faboideae species.

The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination

BackgroundMitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as ‘fossilized’. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms.ResultsAssembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome.ConclusionsThe Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.

Selective constraints in cold-region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes.

Spatial range expansion during population colonization is characterized by demographic events that may have significant effects on the efficiency of natural selection. Population genetics suggests that genetic drift brought by small effective population size (N e) may undermine the efficiency of selection, leading to a faster accumulation of nonsynonymous mutations. However, it is still unknown whether this effect might be balanced or even reversed by strong selective constraints. Here, we used wild boars and local domestic pigs from tropical (Vietnam) and subarctic region (Siberia) as animal model to evaluate the effects of functional constraints and genetic drift on shaping molecular evolution. The likelihood‐ratio test revealed that Siberian clade evolved significantly different from Vietnamese clades. Different datasets consistently showed that Siberian wild boars had lower Ka/Ks ratios than Vietnamese samples. The potential role of positive selection for branches with higher Ka/Ks was evaluated using branch‐site model comparison. No signal of positive selection was found for the higher Ka/Ks in Vietnamese clades, suggesting the interclade difference was mainly due to the reduction in Ka/Ks for Siberian samples. This conclusion was further confirmed by the result from a larger sample size, among which wild boars from northern Asia (subarctic and nearby region) had lower Ka/Ks than those from southern Asia (temperate and tropical region). The lower Ka/Ks might be due to either stronger functional constraints, which prevent nonsynonymous mutations from accumulating in subarctic wild boars, or larger N e in Siberian wild boars, which can boost the efficacy of purifying selection to remove functional mutations. The latter possibility was further ruled out by the Bayesian skyline plot analysis, which revealed that historical N e of Siberian wild boars was smaller than that of Vietnamese wild boars. Altogether, these results suggest stronger functional constraints acting on mitogenomes of subarctic wild boars, which may provide new insights into their local adaptation of cold resistance.

Changes in selection intensity on the mitogenome of subterranean and fossorial rodents respective to aboveground species

Several rodent lineages independently acquired the ability to dig complex networks of tunnels where fossorial and subterranean species spend part or their whole life, respectively. Their underground lifestyles imposed harsh physiological demands, presumably triggering strong selective pressures on genes involved in energy metabolism like those coding for mitochondrial proteins. Moreover, underground lifestyles must have increased inbreeding and susceptibility to population bottlenecks as well as restricted migration, leading to small effective population size (Ne) that, in turn, must have reduced the effectiveness of selection. These stringent environmental conditions and small Ne might be still operating as antagonist factors of selection efficacy in these rodents. In this report, we tested, in a phylogenetic framework, how the intensity of selection on protein-coding mitochondrial genes (mt-genes) fluctuated along the evolution of fossorial and subterranean rodents respective to aboveground lineages. Our findings showed significant selection relaxation in most mt-genes of subterranean hystricomorphs (African mole-rats, tuco-tucos, and coruro), while only in three mt-genes of fossorial hystricomorphs (degus, red vizcacha rat, and fossorial spiny rats) selection efficacy was strongly reduced, probably due to demographic constraints. Conversely, selection intensification was found to have occurred in three mt-genes in fossorial sciuromorphs (ground squirrels, chipmunks, marmot, and allies). Our findings indicated that evolution of mitogenomes in fossorial and, mainly, in subterranean rodents was a complex output of a balance between intense ecological and physiological pressures, together with demographic constraints leading to genetic drift that, in turn, might have resulted in relaxed selection in hystricomorphs.

The Complete Mitochondrial Genome of Ugyops sp. (Hemiptera: Delphacidae).

The complete mitochondrial genome (mitogenome) of Ugyops sp. (Hemiptera: Delphacidae) was sequenced, making it the first determined mitogenome from the subfamily Asiracinae, the basal clade of the family Delphacidae. The mitogenome was 15,259 bp in length with A + T content of 77.65% and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. The gene order was identical with that of the ancestral insect. The nucleotide composition analysis indicated that the whole mitogenome was strongly A-skewed (0.288) and highly C-skewed (−0.270). For PCGs on the J-strand, the AT skew was positive, and the GC skew was negative. All PCGs started with canonical ATN codons, except for cox1 and nad5, which used CTG and GTG as start codon, respectively. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnS1 (AGN), in which the dihydrouridine arm was reduced to a simple loop. The control region included a poly-T stretch downstream of the small rRNA gene (rrnS), a subregion of higher A + T content and tandemly repeated sequence near trnI. The mitogenome of Ugyops sp. could be very helpful in exploring the diversity and evolution of mitogenomes in Delphacidae.