Partial Control Region Research Articles

Population structure and demographic history for year cohort dynamics of landlocked ayu Plecoglossus altivelis altivelis in dam reservoir of Japan.

Ayu Plecoglossus altivelis altivelis is a valuable osmeroid species for inland fishery in Japan. It is classified into two ecological forms of amphidromous migrating between rivers and sea and landlocked migrating between rivers and lakes or dam reservoirs. The number of dams and their reservoirs has remarkably increased in the twenty-first century under climate change, because of their respective roles in hydropower generation with negligible carbon emissions and in flood control. Dam reservoirs therefore become increasingly important as inland nursery grounds of ayu. In this study, we investigated the reproduction status of landlocked ayu migrating in the Haidzuka Dam reservoir and the Tabusa River in western Japan by molecular phylogenetic analysis based on population structure and demographic history for year cohort dynamics. A total of 849 individuals were collected monthly from October 2018 to September 2021 according to an annual life cycle of ayu. Nucleotide sequences of the partial mitochondrial DNA control region yielded 31 haplotypes, consisting of 4 shared haplotypes among the 2019, 2020 and 2021 cohorts and 27 unique haplotypes. The overall haplotype diversity and nucleotide diversity were calculated to be relatively low at 0.3503 ± 0.0206 and 0.0077 ± 0.0045, respectively, suggesting a founder event by dominant haplotypes. Star-shaped radiational haplotypes from dominant shared haplotypes on the median-joining network likely support a founder event. Although pairwise ФST values were determined to be very low among the year cohorts, only the 2019 cohort was found to have a significant difference from the 2020 and 2021 cohorts, for both of which Tajima's D values were also statistically significant. For the overall population, multimodal mismatch distribution and negative Tajima's D and Fu's Fs values in the neutrality test suggested population expansion or population subdivision. The native riverine population in the Tabusa River suffered habitat fragmentation and population bottleneck from dam construction, and therefore severe founder effect remained behind the artificially landlocked population with a low level of genetic diversity in the Haidzuka Dam reservoir.

Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Population structure and phylogeography of the loggerhead sea turtle (Caretta caretta) have so far been assessed mainly by mitochondrial DNA (mtDNA) single-gene sequencing studies. However, phylogenetic relationships amongst matrilines, genetic characterisation of rookeries and mixed-stock analyses have suffered from the limited resolution obtained by comparison of relatively short sequences such as from the mtDNA control region. Whole mitogenome sequencing can significantly improve population genetics, particularly in marine organisms showing female natal philopatry. Despite mitogenomics becoming increasingly common in biodiversity monitoring and conservation, only a few complete mitogenomes are available for C. caretta. In this study, we sequenced the complete mtDNA of 61 loggerhead turtles sampled between 2008 and 2021 along the Italian coastline and central Mediterranean Sea. We assigned complete mtDNA haplotypes to dead embryos and bycatch samples, and introduced a first nomenclature for loggerhead mitogenomes. Analysis of mtDNA diversity, Maximum Parsimony and Bayesian phylogenetic reconstruction allowed improved resolution of lineages with respect to studies reporting on partial mtDNA control region sequence comparisons, and we were able to further inform previous analyses on loggerhead ancestry based on control region haplogroups. Overall, whole mitogenome analysis has potential for considerable improvement of evolutionary history and phylogeographic investigations as well as mixed-stock surveys of loggerhead turtles.

Characterization of the nearly complete mitochondrial genome of ochraceous darkies, Euphaea ochracea Selys, 1859 (Odonata: Zygoptera: Euphaeidae) and phylogenetic analysis

In the present study, the nearly complete mitochondrial genome of Euphaea ochracea was described and its phylogenetic position in the family Euphaeidae was analyzed. Here, we recovered 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a partial control region, resulting in a mitogenome length of 15,545bp. All protein-coding genes were initiated by the typical ATN codon except nad3 and nad1, which utilizes the TTG codon. Four protein-coding genes (cox1, cox2, cox3 and nad5) are terminated by an incomplete stop codon T, while others end with either a TAA or TAG codon. The intergenic spacer region, S5, is absent in this mitogenome, supporting the lack of this region as a specific character in damselflies. Phylogenetic analysis showed that the newly sequenced E. ochracea is phylogenetically closer to E. ornata with a high support value.

Genetic population dynamics of the critically endangered scalloped hammerhead shark (Sphyrna lewini) in the Eastern Tropical Pacific.

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young-of-year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (n= 1818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size-based investigation of population structure and phylogeography of this species in the ETP to date.

Genetic evidence for a single stock of giant tiger prawns Penaeus monodon in demarcated prawn fishing zones of Tanzania

AbstractTanzania demarcated three prawn fishing zones along its coast to spread fishing pressure and help the prawn fishery to recover. However, it is unknown whether the demarcated zones correspond to the genetic stock structure of the world's most commercially important prawn, the giant tiger prawn (Penaeus monodon). Thus, this study used partial mitochondrial control region sequences (534 base pairs) to test the hypotheses that (1) giant tiger prawns in Tanzania's demarcated prawn fishing zones are a single stock and (2) the giant tiger prawns on the Tanzanian coast experienced a recent demographic expansion. The sequences showed high haplotype diversity (h = 0.998–1.0) and low nucleotide diversity (θπ = 1.89%–2.24%). The neutrality test and mismatch analysis showed that the hypothesis of recent demographic expansion could not be rejected. The analysis of molecular variance revealed low and insignificant fixation indices between the zones (FST = 0.00025, p > 0.05; ΦST = −0.00027, p > 0.05), suggesting that the three demarcated fishing zones constitute a single stock and that fishers may be targeting the same stock. Furthermore, it was discovered that Zone 2 has the potential to replenish depleted areas; thus, it should be prioritised in future conservation planning.

Phylogeography of the mesic-adapted striped mouse, Rhabdomys dilectus chakae (Rodentia: Muridae) in forest margins of the Eastern Cape and southern KwaZulu-Natal provinces of South Africa

Abstract Rhabdomys is a genus that occupies a variety of habitats, including forest margins. Among the Rhabdomys taxa, Rhabdomys dilectus chakae has a distribution that covers the eastern seaboard of South Africa, with a poorly defined divergence date from its sister taxon Rhabdomys dilectus dilectus. Here, we study three mitochondrial markers (cytochrome b, cytochrome c oxidase I and partial control region) of R. d. chakae across the Eastern Cape and KwaZulu-Natal forests of South Africa, aiming to determine the cladogenesis (molecular dating) and effective population size of this subspecies through time, in addition to its cladogenesis in relationship to other species within the genus. A phylogenetic analysis revealed six clades within Rhabdomys, confirming that our study area is occupied solely by R. d. chakae, to the exclusion of other recognized sibling species. A fossil-calibrated Bayesian relaxed molecular clock estimated a recent split between R. d. chakae and R. d. dilectus ~1.4 ± 0.35 Mya and between two Rhabdomys pumilio groups, coastal A and B, at 1.16 ± 0.44 Mya. Coalescent Bayesian skyline plots revealed a stable population of R. d. chakae in the study area that was in slow decline until 2500 years ago, when there was an expansion in the late Holocene. Radiation within Rhabdomys dates as far back as 4.27 Mya, and subsequent demographic fluctuations primarily reflect palaeoclimatic changes.

The mitochondrial genome of Mylabris mongolica Dokhtouroff, 1887 (Coleoptera: Meloidae)

Mylabris mongolica Dokhtouroff, 1887 is a traditional medicine material and an important predator in China. The mitochondrial genome of M. mongolica is presented for the first time in this study. The mitogenome is 15,034 bp in length and comprises 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and partial control region. The nucleotide composition of M. mongolica was 36.7% of A, 18.1% of C, 11.1% of G, and 34.1% of T. The phylogenetic results divide all Meloidae species into two clades. The genus Mylabris was retrieved as a paraphyletic group, with Mylabris having a closer relationship with Hycleus than other genera within Meloidae. This study provides useful genetic data for future studies on the phylogeny and evolution of Meloidae species.

Genetic Diversity of HPV 16 and HPV 18 Based on Partial Long Control Region in Iranian Women.

Background Human papillomavirus (HPV) 16 and HPV 18 account for 75% of all cervical cancers. The L1 gene, encoding the major surface protein (MSP), is used to classify HPV types (lineages and sublineages), genotypes, and intratypic variants. Therefore, this study aimed to investigate the lineages, sublineages, genetic variabilities, and mutation effects on transcription factor binding sites by using partial sequences of the HPV 16 and HPV 18 long control regions (LCRs) in these samples. Materials and Methods After DNA isolation from 56 positive samples, the LCR of HPV 16 and HPV 18 were amplified using specific primers, and phylogenetic trees were drawn through MEGA X. Compared to the reference sequences, single nucleotide polymorphisms (SNPs) were identified. The transcription binding sites were also evaluated using the online PROMO database. Results The LCRs of 52 samples were successfully sequenced. Overall, 81.58% of all HPV 16 variants belonged to the D1 sublineage, followed by A4 (13.16%), A1 (2.63%), and C1 (2.63%) sublineages. All HPV 18 isolates belonged to A sublineage, 92.85% to A3 sublineage, and 7.15% to A4 sublineage. Out of 27 SNPs in the HPV 16 LCR, A7382T, T7384G, C7387T, C7393G, A7431G, T7448C, and C7783A were HPV 16-specific. Also, among 14 SNPs in the HPV 18 LCR, C7577A and A7943T were not previously reported. An insertion (C) between 7432 and 7433 positions was identified in all studied HPV 16 variants. Besides, most of the HPV 16 mutations were embedded in the YY1, TFIID, Oct-2, and NF-1 binding sites, while c-Fos and MBF1, as the most common binding sites, were affected by HPV 18 LCR mutations. Conclusion The present results showed that D1 and A3 were the dominant sublineages of HPV 16 and HPV 18, respectively. Therefore, women infected with these variants need to be examined in further longitudinal studies to obtain more information about the oncogenic potential of these dominant variants in Iran. Besides, YY1, TFIID, Oct-2, NF-1, c-Fos, and MBF1 were the most frequent binding sites, which were influenced by the mutations.

Linking Pedigree Information to the Gene Expression Phenotype to Understand Differential Family Survival Mechanisms in Highly Fecund Fish: A Case Study in the Larviculture of Pacific Bluefin Tuna.

Mass spawning in fish culture often brings about a marked variance in family size, which can cause a reduction in effective population sizes in seed production for stock enhancement. This study reports an example of combined pedigree information and gene expression phenotypes to understand differential family survival mechanisms in early stages of Pacific bluefin tuna, Thunnus orientalis, in a mass culture tank. Initially, parentage was determined using the partial mitochondrial DNA control region sequence and 11 microsatellite loci at 1, 10, 15, and 40 days post-hatch (DPH). A dramatic proportional change in the families was observed at around 15 DPH; therefore, transcriptome analysis was conducted for the 15 DPH larvae using a previously developed oligonucleotide microarray. This analysis successfully addressed the family-specific gene expression phenotypes with 5739 differentially expressed genes and highlighted the importance of expression levels of gastric-function-related genes at the developmental stage for subsequent survival. This strategy demonstrated herein can be broadly applicable to species of interest in aquaculture to comprehend the molecular mechanism of parental effects on offspring survival, which will contribute to the optimization of breeding technologies.

Characterization of the mitochondrial genome of Tetrastichus howardi (Olliff 1893) (Hymenoptera: Eulophidae)

The mitochondrial genome has been widely used in the study of phylogeny and species-level evolution. Here, we sequenced and analyzed the full mitogenome of Tetrastichus howardi, an important natural enemy of many lepidopteran pests. The complete mitochondrial genome has 14,791 nucleotides, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a partial control region. All the 13 PCGs started with typical ATN (ATA, ATG, and ATT) codon. Among 13 PCGs, nine genes terminated with the stop codon TAA and four genes terminated with T. Our study provides information on comparative mitogenomics of Eulophidae.

Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system.

Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system - an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.

Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone

We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FSTand SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages ofUrocyonin the United States. Despite broad-scale sampling, we did not recover additional major lineages ofUrocyonwithin the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested withinU. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

Molekularna filogenija i genetička raznolikost domaćih jakova (Bos grunniens) u Pakistanu na temelju mitohondrijskih i mikrosatelitskih markera

The complete Cytchrome b gene and partial mtDNA control region were sequenced for the Pakistani domestic yak (Bos grunniens) within the Bovidae family. A total of 300 samples were genotyped using 27 bovine microsatellite markers from the Gilgit-Baltistan and Skardu regions of Pakistan. We identified a total of 35 mutations and 9 haplotypes based on D-loop sequences, with a haplotype and nucleotide diversity of 0.9640±0.051 and 0.02172±0.00224, respectively. For the Cyt b gene, a total of 23 variable sites and six different haplotypes were observed with 0.885±0.067 haplotype and 0.00989±0.003 nucleotide diversity. Phylogenetic analysis of D-loop and Cyt b gene suggested that domestic yak sequences cluster into two highly divergent maternal lineages (lineages I and II), while three haplogroups A, C, and D were identified of the six previously known haplogroups. Haplogroups A and C were dominant and widely distributed among all investigated yak samples. All microsatellites were polymorphic and a total of 138 alleles were observed, with average polymorphic information content (PIC) of 0.56 indicating their effectiveness. The average heterozygosity was observed at 0.6071 with allele diversity of 5.1111 and gene diversity of 0.4830. The implications of these findings can be applied for yak conservation.

First report of the mitogenome of Hamaxiella brunnescens (Diptera, Tachinidae) from Beijing, China

Hamaxiella brunnescens (Mesnil, 1967) (Diptera, Tachinidae) is a parasitic fly species and of great ecological importance in natural systems as parasitoids of herbivorous insects. The mitogenome of H. brunnescens was sequenced and analyzed here for the first time. The genome is 14,956 bp in length with high A + T content, which consists of 13 protein-coding, 22 tRNA, two rRNA genes, and a partial non-coding control region. The phylogenetic analyses support a monophyletic Tachinidae. The two subfamilies Exoristinae and Phasiinae are fully supported as monophyletic while Tachininae is inferred to be paraphyletic.

Demography of swordfish (Xiphias gladius Linneus) populations from the coasts of Turkey, based on mitochondrial DNA and microsatellites.

The genetic diversity of the Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin, north of the Aegean Sea (Aegean-2013, n=26) and the Mediterranean coast of Turkey (N.Levantine-2013, n=42) were studied genetically, along with ancient samples from Yenikapı excavation (n=6). Partial mitochondrial DNA control region sequences (entire sequences, clade I and clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., Molecular Phylogenetics and Evolution, 2005, 36, 169-187; Viñas et al., ICES Journal of Marine Science, 2010, 67, 1222-1229; Righi et al., Diversity, 2020, 12, 170) from the rest of the Mediterranean Sea. Pair-wise FST and pair-wise AMOVA tests showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the past 20 years. Therefore, the results direct reconsideration of previous descriptions of population sub-structure within the Mediterranean and support high gene flow throughout the region. On the contrary, the results of this study confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One-tailed permutation tests revealed that θ, which is directly proportional to long-term female effective population size (Ne), decreased significantly (P < 0.05) in both regions over the past two decades. On the Turkish coasts, θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. Nonetheless, θ of the ancient sample was consistently and significantly (P < 0.001) higher than those of the eastern and western Mediterranean populations in clade I and clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples, suggesting that the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite-based present Ne estimate of the pooled Aegean-2013 and N.Levantine-2013 populations was lower than 1000 according to the upper limit of 95% c.i. and possibly even lower than 100 according to the mean of posterior distribution of the present Ne estimate calculated by the software package MSVAR. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here show that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need an immediate stringent action and management plan.

Low genetic diversity and no genetic differentiation between maleo hatched at coastal and inland nesting grounds in North Sulawesi, Indonesia

Abstract. Saputra AW, Yuda P. 2020. Low genetic diversity and no genetic differentiation between maleo hatched at coastal and inland nesting grounds in North Sulawesi, Indonesia. Biodiversitas 21: 4772-4777. Maleo Senkawor (Macrocephalon maleo), an endemic and endangered bird of Sulawesi (Indonesia), is burrow-nesting megapodes that incubate its eggs in communal nesting sites in soils heated by sun on beaches and by volcanic activity in inland. The aims of this study were to assess genetic diversity of the Maleo and examine whether those which have different nesting sites have become genetically differentiated. In total, 24 eggshell membranes of Maleo were collected from Tanjung Binerean (coastal nesting ground) and Tambun (inland nesting ground), and the DNA was extracted using silica spin-column kit. PCR was applied to amplify the hypervariable region 1 (HV1) and partial mtDNA control region of HV2 using a specific primer set designed for Maleo. The PCR products were sequenced, resulted in 612 bp, and showed 9 polymorphic sites and 9 haplotypes (H). Further sequences analysis suggested that there was no genetic differentiation between coastal nesting population and inland nesting population (Fst = 0.0009; P = 0.431). As expected, the genetic diversity of Maleo was relatively low (coastal nesting population, Hd: 0.727270, ℼ: 0.002377 and inland nesting population Hd: 0.848480, ℼ: 0.002203).

The mitochondrial genome of Hemipenthes neimengguensis (Diptera: Bombyliidae)

The species of genus Hemipenthes can be easily identified by the following characters: wing with extensive infuscate pattern reaching hind margin basally and at least half as long as wing; antennal flagellum onion-shaped and not segmented; fore tibia smooth or with a few weak bristles. In this study, mitochondrial DNA (mtDNA) of the bee fly, Hemipenthes neimengguensis, has been annotated for the first time in the subfamily. The circular genome is 15,405 bp in length with an A + T content of 72.7%, and contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a partial control region (573 bp). All genes have similar locations and strands with that of other published Diptera. Phylogenetic analysis shows that Hemipenthes neimengguensis + Geron pallipilosus (Bombyliidae) were herein corroborated to be a sister group. And they have very closely related to Leptogaster longicauda and Satanas sp. which belong to the family Asilidae. Our results show the location of genus Hemipenthes in Bombyliidae and the location of the family in Brachycera, and provide data for further study of phylogeny in Diptera.

Novel gene rearrangement in the mitochondrial genome of Pachyneuron aphidis (Hymenoptera: Pteromalidae)

Species in Hymenoptera usually show exceptionally high rates of mitochondrial molecular evolution and dramatic gene rearrangements, which has been attributed to their parasitic lifestyle. However, mitochondrial genome (mitogenome) of chalcidoid wasps is still poorly understood and the evolution of gene rearrangements is still unclear. In this study, the nearly complete mitogenome of Pachyneuron aphidis, a chalcidoid wasp mainly hyperparasitizes the Aphidius gifuensis, was sequenced using a next-generation sequencing strategy. This genome is 15,137 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs and a partial control region. Alignment with other Chalcidoidea mitogenomes revealed a novel inversion in the srRNA-trnV gene cluster in P. aphidis, which is the first of its kind to be reported in Chalcidoidea. Breakpoint distances analysis showed the high value of chalcidoid wasps compare to the ancestral arrangement pattern, which reflected as extensive gene rearrangements. Despite the high frequency of gene rearrangements in these insects, analyses of gene rearrangement and phylogenetic trees showed that species from the same family and the genus tent to have similar gene orders, and the conserved gene blocks (ND3-trnG, srRNA-trnV and COIII-ATP6-ATP8-trnD-trnK-COII-trnL2-COI) can usually be identified, especially at the family level of chalcidoid wasps.

Population genetic structure of Thryssa kammalensis in the Chinese Seas inferred from control region sequences

Thryssa kammalensis (Bleeker, 1849) is a common pelagic species in the Chinese Seas and plays an important role in marine ecosystems. In the present study, 196 individuals of T. kammalensis were collected from nine localities along the Chinese coastal waters. The partial control region sequences of them were sequenced for analysis. Variable numbers of tandem repeats (VNTRs) were common in the control regions of all individuals, which led to variation in sequence length, ranging from 772 to 924 bp. All the populations exhibited high haplotype diversity (0.946–1.000) and low nucleotide diversity (0.015–0.031). Two distinct lineages were identified based on the neighbor-joining (NJ) tree, Bayesian inference (BI) trees, and minimum spanning tree (MST). However, the relative frequency of individuals occupying the two major lineages did not differ significantly among sampling locations. In addition, both molecular variance analysis (AMOVA) and pairwise FST analysis strongly supported little genetic differentiation among populations, revealing no significant genetic structure for T. kammalensis. Neutrality tests and analysis of mismatch distribution suggested that recent population expansion occurred in the two lineages. The climatic changes during Pleistocene periods and dispersal strategy leading to the continual gene flow might have played an important role in the geographical pattern of T. kammalensis.

First mitochondrial genome of a stonefly from the subfamily Microperlinae: Microperla geei (Plecoptera: Peltoperlidae)

The stonefly Microperla geei is the fourth sequenced peltoperlid and the first entire mitochondrial genome of M. geei representing the subfamily Microperlinae. The nearly complete mitogenome of M geei is 15,216 bp in size, has 37 genes and one partial control region, which is the classical structure for insect mitogenome. All PCGs started with ATN, except ND1 and ND5 genes used TTG and GTG. Eleven PCGs used the termination codon TAA or TAG and the COII and ND5 genes stopped with a single T. Our phylogenetic topology tree supported Peltoperlidae was monophyletic and M. geei was a sister-group to the clade (Soliperla sp. + (Cryptoperla stilifera + Peltoperlopsis cebuano)). This study could provide new information for the further phylogenetic studies.