Partial Control Region Research Articles

First mitochondrial genome of a periwinkle from the genus Littoraria: Littoraria sinensis

The nearly complete sequence of the mitochondrial genome of the periwinkle Littoraria sinensis is presented. This is the first mitochondrial genome of the genus Littoraria and the fifth sequenced Littorinidae. The mitogenome of L. sinensis is 16,320 bp in size, with 37 genes and one partial control region. The genes order is identical to those observed in other Littorinidae mitogenomes. The overall base composition shows that AT content (64.76%) is higher than GC content (35.24%). This study should provide new information for the further phylogenetic studies of this species.

The complete mitochondrial genome of Athalia proxima (Hymenoptera: Tenthredinidae) and phylogenetic analysis

The nearly complete mitochondrial genome of Athalia proxima is 15852 bp in size, containing 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a partial control region. Compared to ancestral organization, seven tRNA genes were rearranged. Bayesian and maximum-likelihood trees recovered the monophyly of Tenthredinidae and A. proxima was the basal lineage. The mitogenome sequence provided fundamental data for resolving phylogenetic and genetic problems of Tenthredinidae.

First report of mitogenome of Chinese grass shrimp Palaemonetes sinensis (Crustacea, Decapoda, Palaemonidae) yielded by next-generation sequencing

The nearly complete mitochondrial genome of Palaemonetes sinensis is 15,504 bp in size, containing 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a partial control region. The gene content and arrangement were similar to other Palaemonidae species. The mitogenomic information obtained herein will be useful for future studies on population genetic and phylogenetic analyses of this shrimp.

First report of mitochondrial genome of family Bombyliidae, Geron pallipilosus (Diptera: Bombyliidae)

The species of genus Geron are easily to be found in arid area, more species were reported from Afrontropical than other regions. Their potential use as important pollinators and natural enemy insect, especially in the desert and semidesert region. In this study, the mitochondrial DNA (mtDNA) of the bee fly, Geron pallipilosus, has been annotated for the first time in the family. The circular genome is 15,588 bp in length with an A + T content of 75.5%, and contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and a partial control region (633 bp). All genes have the similar locations and strands with that of other published Diptera. It is the first time to published the whole mitochondrial DNA for the family. Phylogenetic analysis suggests that G. pallipilosus is closely related to Leptogaster longicauda and Satanas sp. which belong to the family Asilidae. Our results show the location of Bombyliidae in the Brachycera, and provide data for further study of phylogeny in Diptera.

Introgression despite protection: the case of native brown trout in Natura 2000 network in Italy

Mediterranean brown trout is subject to several serious threats such as pollution, water abstraction, habitat alteration and especially genetic introgression with domestic strains used for stocking activities. Despite this latter issue has largely been debated by scientists, local managers and stakeholders for decades, official stocking practices with domestic trout still persists in several countries (Italy included), even if there are laws explicitly prohibiting introduction of organisms of non-local origin. Probably, the last opportunity to conserve native brown trout populations is represented by protected areas. Therefore, in the present study, we aimed to verify the role of the Nature 2000 network and a national park as valid tools to guarantee the survival of native brown trout in the Apennines. Partial mitochondrial DNA control region sequence analysis and genotyping of the locus LDH-C1* and 11 microsatellites were used to investigate the genetic diversity of three rivers from central Italy. For all rivers investigated a temporal analysis of introgression was also carried out. The genetic diversity of three domestic stocks was included in the sampling design for comparison. The main results of this study indicated that: (i) the genetic diversity of brown trout in central Italy is very complex and (ii) its conservation is seriously threatened by genetic introgression phenomena still ongoing. The only samples showing no introgression or a decrease in genetic introgression were those isolated by the presence of natural and/or artificial barriers to fish movements rather than protected by inhabiting rivers within the Natura 2000 network. This observation prompts an important reflection on issues concerning fluvial continuity restoration and suggests that barrier removal should be undertaken with caution in order to avoid the concrete risk of domestic trout spreading that could promote additional loss of native brown trout biodiversity.

Genetic analysis of endangered hog deer (Axis porcinus) reveals two distinct lineages from the Indian subcontinent

The hog deer (Axis porcinus) is threatened by habitat alteration, fragmentation, and poaching, which have led to a drastic decline of its wild population. Two subspecies of A. porcinus have been described from its distribution range. A. p. porcinus is reported to occur from Pakistan along the Himalayan foothills through Nepal, India and Myanmar, and A. p. annamiticus is found in Thailand, Indo-China, Laos, Cambodia, and Vietnam. However, the current distribution range of A. p. annamiticus is still unclear. We used the partial control region (CR) of mitochondrial DNA (mtDNA) and seven microsatellite loci to investigate the intra-species structure, differentiation, and demographic history of hog deer populations from three landscapes, the Terai Arc, Northeast, and Indo-Burma (Keibul Lamjao National Park (KLNP), Manipur, India) landscapes. We also carried out divergence time estimation using the complete mitogenome. The level of variation was ~4%, and the time of divergence of the KLNP population and the other Indian populations was about 0.22 Mya, i.e., during the last glaciation periods of the Late Pleistocene/Early Holocene. The KLNP haplotypes of the control region were shared with the Southeast Asian subspecies, A. p. annamiticus. The results of the investigations of the microsatellite loci supported the mtDNA results unambiguously. Two genetically distinct lineages are found in India: one is found from the Terai Arc to Assam (A. p. porcinus) and the other in Manipur (A. p. annamiticus). The genetic diversity in KLNP was low and exhibited a higher degree of genetic differentiation compared with major Indian populations. The Bayesian skyline plots indicated that after a long phase of historic demographic stability, the populations of both the lineages of hog deer suffered pronounced declines during the period from ~800 years BP to 5000 years BP. In summary, our finding provided evidence that the KLNP population is probably a prime, isolated and sustaining stock of A. p. annamiticus and should be managed as evolutionarily significant units (ESUs).

Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA

Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.

Analysis of the nearly complete mitochondrial genome of Paederus fuscipes (Coleoptera: Staphylinidae)

The nearly complete mitochondrial genome of Paederus fuscipes (GenBank accession no. MG581161) is 17,644 bp in size, containing 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a partial control region. The gene order is similar to the typical insect mitochondrial genome. Maximum likelihood tree recovered the monophyly of Staphylininae, Pselaphinae, Paederinae and Aleocharinae. Additionally, Staphylininae is a sister group to Paederinae.

The genetic landscape of Mediterranean North African populations through complete mtDNA sequences

Background: The genetic composition of human North African populations is an amalgam of different ancestral components coming from the Middle East, Europe, south-Saharan Africa and autochthonous to North Africa. This complex genetic pattern is the result of migrations and admixtures in the region since Palaeolithic times.Aims: The objective of the present study is to refine knowledge of the population history of North African populations through the analysis of complete mitochondrial sequences.Subjects and methods: This study has sequenced complete mitochondrial DNAs (mtDNAs) in several North African and neighbouring individuals.Results: The mtDNA haplogroup classification and phylogeny shows a high genetic diversity in the region as a result of continuous admixture. The phylogenetic analysis allowed us to identify a new haplogroup characterised by positions 10 101 C and 146 C (H1v2), a sub-branch of H1v, which is restricted to North Africa and whose origins are estimated as ∼4000 years ago.Conclusions: The analysis of the complete mtDNA genome has allowed for the identification of a North African sub-lineage that might be ignored by the analysis of partial mtDNA control region sequences, highlighting the phylogeographic relevance of mtDNA complete sequence analysis.

Identification of novel haplotypes and interpretation of gene flow of mitochondrial DNA control region of Eurasian otter (Lutra lutra) for the effective conservation.

The number and distribution of Eurasian otters have declined during twentieth century due to human activity and water pollution. The global conservation status of Eurasian otter is presently ‘Near Threatened (NT)’ and strictly protected by being listed on the international legislation and conventions. A number of studies using the mitochondrial DNA (mtDNA) control region (CR) have been conducted in order to effectively apply conservation and reintroduction programs, especially in Europe. However, aside from Europe, there have been few studies concerning genetic diversity and phylogeny of Eurasian otters. Therefore, in this study, we sequenced partial mtDNA CR sequences (232 bp) from five South Korean Eurasian otters and analyzed 27 otters originating from parts of northeast Asia (South Korea, China, Japan and Russia (Sakhalin)), and Europe. Out of 232 bp partial mtDNA CR sequences, 13 polymorphic sites (5.6%) were identified and 4 novel mtDNA CR haplotypes (Lut16–19) were discovered from 12 Eurasian otters originating from northeast Asian region. In this study, a comprehensive analysis of genetic diversity and population structure of Eurasian otter between Europe and northeast Asia continents were conducted. Of these, different past demographic histories in Pleistocene period might have largely impacted the genetic structure of each population differently. In addition, low degree of gene flow, isolation by distance (IBD) pattern from geographically wide distanced dataset and analysis of molecular variance (AMOVA) also represented distinct genetic characteristics of Eurasian otter between Europe and northeast Asia.

Effects of Pleistocene glaciation on the phylogeographic and demographic histories of chub mackerel Scomber japonicus in the north-western Pacific

Pleistocene glacial cycles associated with geological and climatic changes have been suggested to affect the distribution and abundance of marine organisms in the north-western Pacific. In addition to historical processes, several contemporary forces are associated with spatial distributions and genetic structuring of marine species. Herein, we gathered partial mitochondrial control region sequences of chub mackerel Scomber japonicus from 14 localities over most of its geographical range in the north-western Pacific to infer the effect of Pleistocene climatic fluctuations on its historical demography, and to assess the role of historical process and contemporary factors in shaping present-day patterns of genetic differentiation within this species. Phylogeographic patterns revealed two distinct lineages that originated in vicariance during the Middle Pleistocene. However, there was no evidence of phylogeographic partitioning of haplotypes over the sampled range. Population structure analyses indicated a high degree of genetic homogeneity among chub mackerel populations. Demographic analyses indicated both lineages experienced Late Pleistocene population expansion. The observed genetic pattern of chub mackerel is consistent with a scenario of the survival of this species in at least two allopatric glacial refugia during the glacial maxima of the Pleistocene followed by massive dispersals throughout the north-western Pacific and species-specific ecological processes facilitating contemporary gene flow.

Genetic Diversity of an Imperiled Neotropical Catfish and Recommendations for Its Restoration.

The long-whiskered catfish Steindachneridion parahybae (Family Pimelodidae) is endemic to the Paraíba do Sul River basin in southeastern Brazil. This species was heavily exploited by artisanal fisheries and faces challenges posed by dams, introduced species, and deterioration of critical habitat. The remaining populations are small and extirpated from some locales, and the species is listed as critically endangered in Brazil. Screening variation at a partial mitochondrial control region sequence (mtCR) and 20 microsatellite loci, we: (i) describe the patterns of genetic diversity along its current distributional range; (ii) test the null hypothesis of panmixia; (iii) investigate the main factors driving its current population structure, and (iv) propose management of broodstock for fostering recovery of wild populations through genetically cognizant restocking. Our microsatellite data for 70 individuals from five collections indicate moderate levels of heterozygosity (HO = 0.45) and low levels of inbreeding (FIS = 0.016). Individual-based cluster analyses showed clear genetic structure, with three clusters of individuals over the collection area with no mis-assigned individuals, suggesting no recent migration among the three clusters. Pairwise DEST values showed moderate and significant genetic differentiation among all populations so identified. The MUR population may have suffered a recent demographic reduction. mtCRs for 70 individuals exhibited 36 haplotypes resulting from 38 polymorphic sites. Overall, mitochondrial haplotype diversity was 0.930 (±0.023) and nucleotide diversity was 0.011 (±0.002). Significant population structure was observed, with ϕST = 0.226. Genetic markers could be used in a hatchery-based restoration program emphasizing breeding of pairs with low kinship values in order to promote retention of genetic diversity and avoid inbreeding. Individual average kinship relationships showed 87.3% advised matings, 11.0% marginal matings, and 1.7% advised against. While these results comprise a contribution toward planning better breeding management and monitoring, parallel actions to be undertaken include surveying healthy riverine habits for reintroduction and continued searching for wild individuals to introduce new variation into the captive broodstock to avoid adaptation to captivity and to minimize inbreeding.

A mini-primer set in a multiplex PCR fashion covering the MTDNA control region from submerged skeletal remains

When DNA is recovered in a small quantity and low quality, typing methods based on mtDNA should be considered. Mini-primer sets multiplex with reduced amplicons has been successful in amplifying the entire CR. This study developed a mini-primer set PCR multiplex assay to amplify the entire CR of mtDNA from fragments of human skeletal remains submerged in water up to 30, 60 and 90days. So far, the new mini-primer set for PCR multiplex assay was tested on four samples, three of them submerged in river water for a period of 30 months. This approach gave successful PCR amplifications for the three samples submerged and the control. The following sequencing analysis brought partial mtDNA control region profiles to the samples and a complete to the control.

Isolation and characterization of the mitochondrial genome of Gymnodraco acuticeps (Perciformes: Bathydraconidae) with phylogenetic consideration

Gymnodraco acuticepsis is an Antarctic fish living in the Southern Ocean. Until now, studies on G. acuticeps are still limited. As an Antarctic fish, obtaining and characterization of the mitochondrial genome of G. acuticeps will be important for elucidation of the mechanism of cold-adapting evolution in mitochondrion. In this study, we first isolated and characterized the mitochondrial genome sequence of G. acuticeps with 15,987 bp in length. It contained of 34 genes (12 protein-coding genes, 20 transfer RNA genes, 2 ribosomal RNA genes) and a partial putative control region. Gene organization and nucleotide composition of obtained mito-genome were similar to those of other Antarctic fish. Twenty-eight genes were encoded by heavy strand, while six genes were encoded by light strand. Further, the phylogenetic tree, which based on 12 protein-coding genes, revealed that the G. acuticeps was genetically closest to species Parachaenichthys charcoti among 18 species. We hope this work would be helpful for the population genetics and molecular evolution studies.

The mitochondrial genome of Mesocapnia daxingana (Plecoptera: Capniidae)

The stonefly Mesocapnia daxingana (Plecoptera: Capniidae) is a new species and the capniid genus Mesocapnia are first reported from China. Their potential use as biomonitoring for water quality assessment is well-known. In this study, we present the mitogenome of M. daxingana, which is 15,524 bp in length and consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs and a partial control region (719 bp). All genes have the similar locations and strands with that of other published stoneflies. The nucleotide composition is biased toward A and T, with 68.1% of A + T content. Phylogenetic analysis suggests that M. daxingana is closely related to Mesocapnia arizonensis and Apteroperla tikumana. Both maximum likelihood and Bayesian inference analyses showed strong support for a monophyletic Capniidae, and other five stonefly family formed a monophyletic group.

The mitochondrial genomes of Atlas Geckos (Quedenfeldtia): mitogenome assembly from transcriptomes and anchored hybrid enrichment datasets

The nearly complete mitogenomes of the two species of North African Atlas geckos, Quedenfeldtia moerens and Q. trachyblepharus were assembled from anchored hybrid enrichment data and RNAseq data. Congruent assemblies were obtained for four samples included in both datasets. We recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for both species, including partial control region. The order of genes agrees with that of other geckos.

The taxonomic status of badgers in the Qinghai Lake area and evolutionary history of Meles

To investigate the phylogenetic status of badgers (Meles sp.) in the Qinghai Lake area and to estimate the divergence time within Eurasian badgers, the cytochrome b gene and the partial control region (CR) of mitochondrial DNA were examined as genetic markers. Our results indicated that Meles is divided into four species. Twenty one haplotypes were identified in 23 combined sequences (1,652 bp) of Cyt b and CR sequences. Results showed that Eurasian badgers were clearly divided into two major lineages: one of Western lineage, composed of badgers from Europe and Southwest Asia, and the other of Eastern lineage, composed of badgers from North and East Asia (including Japan). Furthermore, the Bayesian tree and the haplotype network indicated that the badgers in the Qinghai Lake area are Asian badgers (M. leucurus). The estimated divergence time was consistent with palaeontological evidence. The first split between the Western lineage and Eastern lineage occurred approximately 2.24 Ma. After the separation, the Southwest Asia clade split from Europe approximately 1.27 Ma and the Japan clade split from continental Asia approximately 0.99 Ma.

Evidence of male-biased dispersal in eastern grey kangaroos (Macropus giganteus)

Dispersal reduces the likelihood of inbreeding and maintains gene flow among populations. Many polygynous mammals exhibit male-biased dispersal with female philopatry. Previous observational studies of eastern grey kangaroos (Macropus giganteus) suggested female philopatry while genetic studies showed weak structuring. We tested for sex-biased dispersal using two Queensland populations of kangaroos: one in Sundown National Park and the second at Elanda Point, Australia. Samples from 25 females and 23 males were collected from Sundown National Park, and analysed for partial mtDNA control region sequences (n = 47) and genotypes based on 12 microsatellite loci (n = 41). Samples from 18 males and 22 females from Elanda Point were genotyped at 8 loci and a subset sequenced for mtDNA (n = 19). Analyses showed higher mtDNA haplotype and nucleotide diversity in males than females within both populations, genetic relatedness based on microsatellite data was significantly higher among females, and microsatellite allelic richness was higher in males, suggesting that females are more likely to be philopatric and males more likely to disperse. These findings reinforce the value of including multiple types of genetic markers in dispersal analyses as mtDNA results showed higher male diversity (suggesting male dispersal) but males also contributed microsatellite alleles to the local population, masking differentiation between the sexes and confounding analyses.

The nearly complete mitochondrial genome of Chinese pygmy dormouse Typhlomys cinereus (Rodentia: Platacanthomyidae)

In this study, we report the nearly complete mitochondrial genome of a Chinese pygmy dormouse Typhlomys cinereus (Rodentia: Platacanthomyidae). The 15,011 bp genome is consisted of 13 protein-coding genes, 16S rRNA, 21 tRNAs, partial 12S rRNA and control region. A phylogenetic tree was built using 12 protein-coding genes of 19 species from Dipodoidea and Muroidea. Our result shows that T. cinereus represents the earliest split within Muroidea. The genome would contribute to further study of phylogeny in Muroidea and Rodentia.

The near complete mitochondrial genome of the Giant honey bee, Apis dorsata (Hymenoptera: Apidae: Apinae) and its phylogenetic status

In this report, we sequenced and characterized the near complete mitochondrial genome of Apis dorsata collected from Mizoram, India. For sequencing of the complete mitochondrial genome, Illumina NextSeq500 platform was used. The near complete mitochondrial genome was assembled to be 15 076 bplong and contains the same gene order as the other honey bees. The assembly contains 13 protein coding genes, 21 transfer RNA, 2 ribosomal RNA and a partial control (A + T-rich) region estimated to be 75 bp. This is the first near complete sequenced mitochondrial genome from the giant honeybee A. dorsata which will benefit future genomics studies for understanding the phylogenetic relationship within the bee family.