16S mtDNA Research Articles

Pregestational screening of hereditary deafness genes carriers in 10,684 normal pregnant women in Zhuzhou, China.

Mutations in genes associated with deafness differ between ethnic groups and regions in China. In this study, we investigated the genes associated with deafness in pregnant women to analyze the distribution of mutations leading to deafness in Zhuzhou, China. A total of 10,684 pregnant women were enrolled in this study. DNA samples were collected to detect the 14 common mutations in deafness genes (at 108 sites). Prevalence of mutations in deafness genes in pregnant women with normal hearing in Zhuzhou was 4.92% (526/10,684). Among these 526 pregnant women with deafness gene mutations, the frequencies of mutated GJB2, GJB3, SLC26A4, and mtDNA 12S rRNA were 40.11, 7.22, 40.68, and 11.98%, respectively. The hotspots for mutations in the deafness genes were: c.235delC in GJB2 (31.18%), c.919-2A > G in SLC26A4 (18.44%), c.299_300delAT in GJB2 (5.70%), m.7444G > A in mtDNA 12S rRNA (5.70%), c.1229C > T in SLC26A4 (5.51%), m.1555A > G in mtDNA 12S rRNA (5.32%), accounting for 71.85%. Moreover, husbands of the 526 pregnant women who carried the deafness gene mutations were also included in the analysis to detect deafness gene mutations. Among the 526 husbands, 23 husbands carried mutations in deafness genes, accounting for 4.37%. The deafness gene mutations of the husbands and pregnant wives were not the same. In addition, the results of the neonatal follow-up hearing tests were all normal. Our study identified the prevalence of mutations in GJB2, SLC26A4, mtDNA 12S rRNA, and GJB3 genes in pregnant women from Zhuzhou, China.

Single-locus species delimitation and ecological niche modelling provide insights into the evolution, historical distribution and taxonomy of the Pacific chorus frogs

AbstractThe Pacific chorus frogs are a complex of three wide-ranging species (i.e. Hyliola hypochondriaca, Hyliola regilla, Hyliola sierra) whose current taxonomy remains unresolved. We conducted species delimitation analyses of these taxa using fragments of the cytochrome b and 12S–16S mtDNA genes to assess the species diversity. Importantly, we included samples from new locations throughout the range to better understand species distributions and identify potential contact zones among clades. Our analyses revealed three slightly parapatric but distinct species-level clades. Molecular dating revealed that these species began diverging in the Pleistocene c. 1.4 Mya with H. hypochondriaca and H. sierra diverging more recently c. 0.8 Mya. We found that populations from western Montana and Idaho originated recently from populations to the southwest that belong to H. sierra, rather than from H. regilla populations directly to the west. Population sizes of each species expanded c. 130–80 Kya with H. hypochondriaca exhibiting a more pronounced expansion beginning c. 100 Kya than the more gradual expansion of the other two species. The climatic niche models suggest that distributions of the three species were similar during the last interglacial (LIG) as they are today. During the Last Glacial Maximum (LGM), H. hypochondriaca and H. sierra occupied a larger range than they do today whereas H. regilla occupied a smaller refugium, shifted south from the current distribution. This study highlights the continued effectiveness of utilizing single-locus data sets for species delimitation and biogeographic analyses.

Phenotypic and genetic variation of Triatoma costalimai (Hemiptera: Reduviidae).

INTRODUCTION: We aimed to study intraspecific variation in Triatoma costalimai, a potential vector of Chagas disease present in Brazil and Bolivia. METHODS: We analyzed phenotypic (connexivum color patterns, wing morphometrics) and genetic variation (16S mtDNA) of three Brazilian T. costalimai populations. We compared 16S sequences with those of putative Bolivian T. costalimai and its sister species, T. jatai. RESULTS: Brazilian populations had different connexivum color patterns and forewing shapes. A 16S mtDNA haplotype network showed a clear separation of Brazilian T. costalimai from both T. jatai and Bolivian T. costalimai. CONCLUSIONS: We report considerable variability in T. costalimai populations.

A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America.

BackgroundStudies with integrative approaches (based on different lines of evidence) are fundamental for understanding the diversity of organisms. Different data sources can improve the understanding of the taxonomy and evolution of snakes. We used this integrative approach to verify the taxonomic status of Hydrodynastes gigas (Duméril, Bibron & Duméril, 1854), given its wide distribution throughout South America, including the validity of the recently described Hydrodynastes melanogigas Franco, Fernandes & Bentim, 2007.MethodsWe performed a phylogenetic analysis of Bayesian Inference with mtDNA 16S and Cytb, and nuDNA Cmos and NT3 concatenated (1,902 bp). In addition, we performed traditional morphometric analyses, meristic, hemipenis morphology and coloration pattern of H. gigas and H. melanogigas.ResultsAccording to molecular and morphological characters, H. gigas is widely distributed throughout South America. We found no evidence to support that H. gigas and H. melanogigas species are distinct lineages, therefore, H. melanogigas is a junior synonym of H. gigas. Thus, the melanic pattern of H. melanogigas is the result of a polymorphism of H. gigas. Melanic populations of H. gigas can be found in the Tocantins-Araguaia basin.

Unraveling elephant-shrews: Phylogenetic relationships and unexpected introgression among giant sengis

Giant sengis, or elephant-shrews (Macroscelidea; Macroscelididae; Rhynchocyon), are small-bodied mammals found in central and eastern African forests. Studies have provided contrasting views of the extent and direction of introgression among species. We generated full mitochondrial genomes, and compiled publically available mtDNA 12S and nuclear vWF sequences from Rhynchocyon cirnei, R. petersi and R. udzungwensis that had not previously been analyzed in concert, to elucidate the phylogenetic and population-specific context of potential introgression. Our spatially and phylogenetically broad sampling across species revealed substantial, unidirectional mitochondrial introgression of the R. petersi lineage into R. cirnei reichardi and R. udzungwensis, and from R. udzungwensis into R. c. reichardi. All introgression was highly localized and found only in the eastern Udzungwa Mountains forests in Tanzania. The nuclear data showed another pattern, with R. petersi haplotypes in R. cirnei cirnei and R. c. reichardi. No individuals showed both mitochondrial and nuclear introgression. Our results suggest higher levels of hybridization among giant sengi species than previously recognized, but also highlight the need for further genome-wide analysis and increased spatial sampling to clarify the many aspects of diversification and introgression in this group.

A new genus and species from Brazil of the resurrected family Macromaxillocarididae Alvarez, Iliffe & Villalobos, 2006 and a worldwide list of Stenopodidea (Decapoda)

AbstractA new genus and species, Chicosciencea pernambucensisgen. nov., sp. nov., is described from two localities along the coast of Pernambuco state, northeastern Brazil. Considering the unresolved situation of the families of Stenopodidea in previous studies, the position of this new genus is discussed based on morphological, molecular (16S mtDNA), and ecological data. The morphological analysis revealed that Chicoscienceagen. nov. differs from all stenopodidean genera by a combination of characters. The inferred molecular phylogeny recovered a monophyletic group including Chicoscienceagen. nov., MacromaxillocarisAlvarez, Iliffe & Villalobos, 2006, and MicroprosthemaStimpson, 1860, which comprise free-living (i.e., not-sponge associated), shallow-water species. Based on this monophyletic group and on their morphological and ecological similarities, we herein formally propose the resurrection of Macromaxillocarididae Alvarez, Iliffe & Villalobos, 2006 to include those genera. We also provide an updated world list of Stenopodidea. With the description of Chicoscienceagen. nov., the infraorder Stenopodidea now comprises 13 genera and 92 species.

Molecular phylogeny and classification of the family Myxinidae (Cyclostomata: Myxiniformes) using the supermatrix method

Many aspects of myxinid taxonomy remain poorly understood, particularly at the genus and subfamily levels. To clarify the validity of two genera (Paramyxine and Notomyxine) and two subfamilies (Rubicundinae and Myxininae), we used a novel supermatrix approach to reconstruct large phylogenies, combining mtDNA (16S rRNA + cytochrome c oxidase subunit 1) and ncDNA data (18S rRNA + 28S rRNA). We firstly revealed that the genus Notomyxine is considered as a synonym of the genus Myxine. In addition, our findings supported the study of Fernholm et al (2013) that genus Paramyxine is considered as a synonym of genus Eptatretus in Eptatretinae, and the monophyly of Rubicundinae. Within subfamily Myxininae, we confirmed that the genus Neomyxine is separated from the other Myxininae and firstly branched into the basal position of all Myxinidae. In the future study to establish a new subfamily, the genus Nemamyxine as well as genus Neomyxine species will be reviewed by examination of type specimens and analysis of various molecular data.

Tachiramantis lassoalcalai (Barrio-Amorós, Rojas-Runjaic amp; Barros, 2010) (Anura, Craugastoridae): a new combination revealed by molecular evidence, with a description of its advertisement call.

Pristimantis lassoalcalai Barrio-Amorós, Rojas-Runjaic Barros, 2010 is a poorly known terrarana, endemic to the eastern slope of Sierra de Perijá in Venezuela. Although a close relationship of this species with Tachiramantis has been suspected based on its overall morphological similarity, this relationship had not been tested so far. On the basis of molecular data (two fragments of the 12S and 16S mtDNA genes) obtained from the type series, we reconstruct its evolutionary relationships and establish its phylogenetic position as a member of Tachiramantis. Based on this phylogenetic hypothesis, we transfer Pristimantis lassoalcalai to Tachiramantis as Tachiramantis lassoalcalai comb. nov. In addition, we describe its advertisement call. This is the fourth known species of the genus and the second to which its vocalization is described.

Divergent domains of 28S ribosomal RNA gene: DNA barcodes for molecular classification and identification of mites

BackgroundThe morphological and molecular identification of mites is challenging due to the large number of species, the microscopic size of the organisms, diverse phenotypes of the same species, similar morphology of different species and a shortage of molecular data.MethodsNine medically important mite species belonging to six families, i.e. Demodex folliculorum, D. brevis, D. canis, D. caprae, Sarcoptes scabiei canis, Psoroptes cuniculi, Dermatophagoides farinae, Cheyletus malaccensis and Ornithonyssus bacoti, were collected and subjected to DNA barcoding. Sequences of cox1, 16S and 12S mtDNA, as well as ITS, 18S and 28S rDNA from mites were retrieved from GenBank and used as candidate genes. Sequence alignment and analysis identified 28S rDNA as the suitable target gene. Subsequently, universal primers of divergent domains were designed for molecular identification of 125 mite samples. Finally, the universality of the divergent domains with high identification efficiency was evaluated in Acari to screen DNA barcodes for mites.ResultsDomains D5 (67.65%), D6 (62.71%) and D8 (77.59%) of the 28S rRNA gene had a significantly higher sequencing success rate, compared to domains D2 (19.20%), D3 (20.00%) and D7 (15.12%). The successful divergent domains all matched the closely-related species in GenBank with an identity of 74–100% and a coverage rate of 92–100%. Phylogenetic analysis also supported this result. Moreover, the three divergent domains had their own advantages. D5 had the lowest intraspecies divergence (0–1.26%), D6 had the maximum barcoding gap (10.54%) and the shortest sequence length (192–241 bp), and D8 had the longest indels (241 bp). Further universality analysis showed that the primers of the three divergent domains were suitable for identification across 225 species of 40 families in Acari.ConclusionsThis study confirmed that domains D5, D6 and D8 of 28S rDNA are universal DNA barcodes for molecular classification and identification of mites. 28S rDNA, as a powerful supplement for cox1 mtDNA 5’-end 648-bp fragment, recommended by the International Barcode of Life (IBOL), will provide great potential in molecular identification of mites in future studies because of its universality.

Genetic uniformity, geographical spread and anthropogenic habitat modifications of lymnaeid vectors found in a One Health initiative in the highest human fascioliasis hyperendemic of the Bolivian Altiplano

BackgroundFascioliasis is a snail-borne zoonotic trematodiasis emerging due to climate changes, anthropogenic environment modifications, and livestock movements. Many areas where Fasciola hepatica is endemic in humans have been described in Latin America altitude areas. Highest prevalences and intensities were reported from four provinces of the northern Bolivian Altiplano, where preventive chemotherapy is ongoing. New strategies are now incorporated to decrease infection/re-infection risk, assessment of human infection sources to enable efficient prevention measures, and additionally a One Health initiative in a selected zone. Subsequent extension of these pilot interventions to the remaining Altiplano is key.MethodsTo verify reproducibility throughout, 133 specimens from 25 lymnaeid populations representative of the whole Altiplano, and 11 used for population dynamics studies, were analyzed by rDNA ITS2 and ITS1 and mtDNA cox1 and 16S sequencing to assess their classification, variability and geographical spread.ResultsLymnaeid populations proved to belong to a monomorphic group, Galba truncatula. Only a single cox1 mutation was found in a local population. Two cox1 haplotypes were new. Comparisons of transmission foci data from the 1990’s with those of 2018 demonstrated an endemic area expansion. Altitudinal, northward and southward expansions suggest movements of livestock transporting G. truncatula snails, with increasing temperatures transforming previously unsuitable habitats into suitable transmission areas. Transmission foci appear to be stable when compared to past field observations, except for those modified by human activities, including construction of new roads or control measures undertaken in relation to fascioliasis.ConclusionsFor a One Health initiative, the control of only one Fasciola species and snail vector species simplifies efforts because of the lower transmission complexity. Vector monomorphism suggests uniformity of vector population responses after control measure implementation. Hyperendemic area outer boundary instability suggests a climate change impact. All populations outside previously known boundaries were close to villages, human dwellings and/or schools, and should therefore be considered during disease control planning. The remarkable southward expansion implies that a fifth province, Aroma, should now be included within preventive chemotherapy programmes. This study highlights the need for lymnaeid molecular identification, transmission foci stability monitoring, and potential vector spread assessment.

A new species of the genus Zhangixalus (Amphibia: Rhacophoridae) from Vietnam

ABSTRACT A new rhacophorid species is described from Vietnam on the basis of nine specimens collected in Quan Ba District, Ha Giang Province, northeastern Vietnam. The new species is morphologically similar to Zhangixalus pinglongensis, Z. dorsoviridis, and Z. nigropunctatus, however, it differs from the latter by having the flank cream with large black blotches on axilla and groin. The genetic distance between the new species and Zhangixalus pinglongensis, Z. dorsoviridis and Z. nigropunctatus is >3.57% (16S mtDNA gene fragment). Zhangixalus jodiae sp. nov. can be distinguished from all other species of Zhangixalus and other small rhacophorid species from Southeast Asia by a combination of the following characters: size small (SVL 36.1–39.8 mm in males); head as long as wide; vomerine teeth present; dorsal surface of head and body green without spots; axilla cream with large black blotches, groin and front-rear parts of the thigh, ventral surface of tibia black with orange blotches; lower jaw region greyish, chest and belly cream. http://www.zoobank.org/urn:lsid:zoobank.org:pub:89597718-024F-4FFC-B0AE-2005F12CF66C

Multiplex PCR assay for animal species identification in meat bone meal

The authenticity of meat bone meal (MBM) in animal feed is needed to be considered due to inappropriate feed ingredients for certain types of livestock may cause various diseases. This work was aimed to identify animal species in MBM using multiplex PCR assay with 12S rRNA gene as a target region. Total of eight DNA samples were extracted from three species (chicken, bovine, and porcine) which are used as positive controls and three MBM samples. The MBM samples were collected from three different importers. Additionally, a multiplex PCR assay has been performed to identify animal species in MBM. Multiplex PCR of 12S rRNA gene was designed to detect bovine, chicken, and porcine in MBM samples. The PCR products was visualized using 2% agarose gels under the UV light. The results showed that multiplex-PCR of 12S rRNA gene was able to identify bovine which is indicated by 155 bp of DNA band. Chicken and porcine were not found in MBM samples. Meat bone meal samples used in this study might be used to be a feedstuff for poultry, porcine, and other non-ruminants. In conclusion, Multiplex-PCR using mt-DNA 12S rRNA was effective and accurate technique to identify species contained in MBM samples.

An enhanced DNA amplification method to detect the species origins of the rootless hair shafts

Hairs are commonly encountered at crime scenes. Determining the biological origins of hairs is important for case investigations. However, the DNA extraction of rootless hair shafts are quite difficult. In this study, an enhanced DNA amplification methodology is revealed, in combination with a self-developed system of 5 × PCR Reaction Master Mix IV, to directly amplify the mtDNA 12S ribosomal RNA (12S rRNA) gene from rootless hair shafts collected from 12 common species (human, chicken, duck, cattle, sheep, dog, mouse, pig, horse, cat, rabbit and pigeon) without DNA extraction. The amplicons were subsequently sequenced on Pyromark Q48 (QIAGEN, Hilden, Germany). The results illustrated that the direct amplification system could efficiently amplify the targeted mtDNA genes and pyrosequencing technology could further readily differentiate the sample origin of the rootless hair shafts. Data analysis of the 12S rRNA was equipped to an automatic analysis module. This study provides a new solution for species identification of rootless hair shafts.

Concurrent Hearing and Genetic Screening of 180,469 Neonates with Follow-up in Beijing, China

Concurrent hearing and genetic screening of newborns is expected to play important roles not only in early detection and diagnosis of congenital deafness, which triggers intervention, but also in predicting late-onset and progressive hearing loss and identifying individuals who are at risk of drug-induced HL. Concurrent hearing and genetic screening in the whole newborn population in Beijing was launched in January 2012. This study included 180,469 infants born in Beijing between April 2013 and March 2014, with last follow-up on February 24, 2018. Hearing screening was performed using transiently evoked otoacoustic emission (TEOAE) and automated auditory brainstem response (AABR). For genetic testing, dried blood spots were collected and nine variants in four genes, GJB2, SLC26A4, mtDNA 12S rRNA, and GJB3, were screened using a DNA microarray platform. Of the 180,469 infants, 1,915 (1.061%) were referred bilaterally or unilaterally for hearing screening; 8,136 (4.508%) were positive for genetic screening (heterozygote, homozygote, or compound heterozygote and mtDNA homoplasmy or heteroplasmy), among whom 7,896 (4.375%) passed hearing screening. Forty (0.022%) infants carried two variants in GJB2 or SLC26A4 (homozygote or compound heterozygote) and 10 of those infants passed newborn hearing screening. In total, 409 (0.227%) infants carried the mtDNA 12S rRNA variant (m.1555A>G or m.1494C>T), and 405 of them passed newborn hearing screening. In this cohort study, 25% of infants with pathogenic combinations of GJB2 or SLC26A4 variants and 99% of infants with an m.1555A>G or m.1494C>T variant passed routine newborn hearing screening, indicating that concurrent screening provides a more comprehensive approach for management of congenital deafness and prevention of ototoxicity.

Biological inventory of Ranomafana National Park tetrapods using leech-derived iDNA

The terrestrial blood feeding leeches of family Haemadipsidae are abundant throughout the Indo-Pacific, a region which encompasses many of the world’s biodiversity hotspots. Haemadipsids have been shown to retain high-quality host DNA in their guts on the order of months and have been targeted as tools for vertebrate biodiversity assessment in tropical rainforests, where species are difficult to monitor. Complementing prior mammal-specific 16S mtDNA data, the 12S mtDNA locus optimized for tetrapods was employed to assign identities to leech hosts. Through traditional Sanger sequencing of each blood meal for each of 16S and 12S mitochondrial regions, we find a 41% increase in the diversity of taxa detected using both loci than of using 16S alone. In addition to mammalian diversity assigned through sequencing of 16S, the host identities determined through sequencing of both loci inform the diversity of sampled localities as well as the foraging behavior of the leeches themselves. We present evidence for generalist foraging among the terrestrial leeches of Madagascar (Chtonobdella fallax), with data suggesting mammals, birds, amphibians, and reptiles as viable leech hosts.

Diversity of the Bosmina (Cladocera: Bosminidae) in China, revealed by analysis of two genetic markers (mtDNA 16S and a nuclear ITS)

BackgroundChina is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton. Bosmina, a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of Bosmina across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the Bosmina across China was investigated using molecular tools for the first time.ResultsTwo main species were detected in 35 waterbodies: an endemic east Asia B. fatalis, and the B. longirostris that has a Holarctic distribution. B. fatalis had lower genetic polymorphism and population differentiation than B. longirostris. B. fatalis was preponderant in central and eastern China, whereas B. longirostris was dominated in western China. The third lineage (B. hagmanni) was only detected in a reservoir (CJR) of eastern China (Guangdong province). Bosmina had limited distribution on the Tibetan plateau.ConclusionsThis study revealed that the biogeography of Bosmina appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).

Metabarcoding analysis of the Pacific harbor seal diet in Mexico

Massive sequencing has improved the predator diet analysis, making it possible to identify taxa with low or no detectability via traditional scatological methods. In Mexico, the Pacific harbor seal (Phoca vitulina richardii) diet has been understudied, with the importance of invertebrates or cartilaginous fish as prey currently unknown. This study aims to characterize the harbor seal diet through metabarcoding and to compare results with those obtained via the analysis of the hard remains taken from the same samples. Samples were collected at four breeding colonies during the molting season. Libraries were constructed following an Illumina dual-indexed strategy using specific eukaryote (18S rRNA), chordate and cephalopod (16S mtDNA) primers to amplify the prey’s DNA, and blocking primers to avoid predator DNA amplification. Libraries were sequenced on the MiSeq® platform (Illumina), generating 848,411 reads. The quality control and taxonomic assignment for the sequences were performed in silico using bioinformatic tools. The present study, identified 49 prey (mostly bony fish), including 14 species of invertebrates, hagfish, and elasmobranchs, thus widening knowledge of the Pacific harbor seal’s diet. While 19 prey species were identified using both the hard remains and metabarcoding analysis, methods (with only four identified to genus level), lower prey richness was found in the hard remains. The main prey items around all islands were longfin sanddab (Citharichthys xanthostigma) and California lizardfish (Synodus lucioceps). Metabarcoding analysis is a new approach for studying the diet of key species in a highly productive and changing ecosystem, such as the California Current System.

Identification of novel variants in MYO15A, OTOF, and RDX with hearing loss by next-generation sequencing.

BackgroundNonsyndromic hearing loss (NSHL) is the most common sensorineural disorder and one of the most common human defects. Autosomal recessive inheritance accounts for a huge percentage of familial cases. Next‐generation sequencing (NGS) is a powerful molecular diagnostic strategy for NSHL. The combination of a microarray gene chip and NGS can better delineate the etiology and genetic cause of deafness in many cases.MethodsOne hundred and thirty‐one unrelated students with NSHL who attend a special education school in Yunnan Province were recruited. Firstly, four common deafness‐related genes (GJB2, GJB3, SLC26A4, and mtDNA 12S rRNA) were evaluated for mutations using a microarray kit. Furthermore, 227 known human deafness genes were sequenced to identify the responsible genetic variant of the proband in three Chinese families with autosomal recessive hearing loss. The mutational status of family members of the probands was validated by Sanger sequencing.ResultsFive novel variants were found in three families using NGS. In family 1, we identified compound heterozygosity at the MYO15A (OMIM, #600316), including an duplication variant c.3866dupC, p.His1290Alafs*25 and a 3‐bp deletion (c.10251_10253del, p.Phe3420del), resulting in protein length changes and premature protein truncation, respectively. In family 2, two affected siblings from a consanguineous Chinese Dai family harbored an c.1274G>C, p.Arg425Pro missense variant in the OTOF (OMIM, #601071). In family 3, we identified compound heterozygosity for c.129_130del, p.His43Glnfs*28 and c.76_79del, p.Lys26* in the RDX gene (OMIM, #611022).ConclusionFive novel variants were found in three families with NSHL. Our findings extend the mutational spectrum in deafness‐related genes and will help physicians in better understanding the etiology of hearing loss.

Parallel evolution of an alpine type ecomorph in a scorpionfly: Independent adaptation to high‐altitude environments in multiple mountain locations

Elucidation of the diversification process of organisms is one of the important tasks of biology. From the viewpoint of species diversity, insects are the most successful group among the diverse organisms on earth and evolutionary adaptation is one of the important factors driving this pattern. Evolutionary adaptation is one of the important factors in the diversification of insects. One of the representative examples of environmental adaptation in insects is the shortening and loss of wings in subalpine and alpine zones. In this study, we focused on the Japanese scorpionfly, Panorpodes paradoxus. In this species, individuals that inhabit mountainous regions and subalpine zones have long wings (the "general type"), and individuals that inhabit higher altitudinal ranges have short wings (the "alpine type"). We collected samples of all Japanese Panorpodes species and one Korean Panorpodes species, and conducted molecular phylogenetic analyses of the mtDNA COI (610bp), COII (688bp), and 16S rRNA (888bp) and nuDNA EF1-α (658bp) and 28S rRNA (524bp) regions in order to reveal the evolutionary history of the alpine type of P.paradoxus. As a result of molecular phylogenetic analyses, it was revealed that the alpine type of P.paradoxus was polyphyletic, and had evolved to become the alpine type at least twice independently at separate mountain locations. In addition, the result of divergence time estimation suggested that the alpine type is an "ecomorph", having recently adapted to low temperature habitats following mountain uplift within the Japanese Archipelago and subsequent glacial-interglacial cycles.

Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA.

The objective of this research was to characterize the genetic diversity and phylogenetic diversity among 12 cattle breeds (10 Chinese breeds and two foreign taurine breeds as controls) utilizing gene mtDNA 16S rRNA. The complete sequences of the mtDNA 16S rRNA genes of the 251 animals were 1570 bp long. The mean percentages of the four nitrogen bases were 37.8 % for adenine (A), 23.7 % for thymine (T), 20.9 % for cytosine (C), and 17.6 % for guanine (G). The mtDNA 16S rRNA gene base percentages had a strong bias towards A T. All detected nucleotide variations in gene mtDNA 16S rRNA were either transitions (62.3 %) or transversions (37.7 %); no indels (insertions and deletions) were found. A total of 40 haplotypes were constructed based on these mutations. A total of 36 haplotypes of these 40 haplotypes were present in 10 Chinese cattle breeds. The haplotype diversity of all Chinese cattle populations was , while the nucleotide diversity was . Kimura's two-parameter genetic distances between pairs of the studied 12 breeds ranged from 0.001 to 0.010. The phylogenetic analysis assigned the 10 Chinese breeds to two distinct lineages that likely differed in their percentage of Bos taurus and Bos indicus ancestry.