mtDNA Fragments Research Articles

A new D-Loop mitochondrial nucleotide variation from individual at Naga and Kuta traditional village

The D-Loop region of human mitochondrial DNA (mtDNA) has a higher level of polymorphism compared to nuclear DNA. Therefore, the mtDNA D-Loop area can determine a particular individual or ethnic identity. This study aims to determine the variation of the D-Loop region nucleotide sequence, namely the Hipervariable I (HV1) region in normal tribal individuals in Kampung Naga and Kampung Kuta. The sample used is the hair root. In determining the variation of nucleotides has been carried out a series of stages of research, namely the isolation of mitochondrial DNA from hair root samples using buffer lysis, mtDNA sample amplification using PCR techniques with M1 primers and HV2R primers, detection of D-Loop region mtDNA fragments by agarose gel electrophoresis, and sequencing of PCR products by the Sanger Dideoxy method and nucleotide sequence analysis of the sequencing results. The results of DNA amplification by PCR showed a band in the area of 1.0 kb. Homology analysis was carried out by comparing the nucleotide sequences of samples with the Cambridge nucleotide sequence, which shows that there are 10 variations. The new variation (morph) is determined by comparing the results of the variations of the two samples with variations from Homo Sapiens Indonesia including Baduy, Sundanese, Javanese (Sangiran), and Madura. Homology results showed 4 new variations, namely c(16184)A, t(16209)C, a(16272)G, t(16519)C. Sapiens Kuta village and Sundanese (general) have a close genetic relationship. The ancestors of the two Homo Sapiens were closely related to Homo Sapiens Naga, Homo Sapiens Naga are closely related to the Homo Sapiens of the Baduy. The ancestors of Homo sapiens, Kuta, Sundanese, Naga and Baduy, are closely related to Homo sapiens Sangiran (Java). Homo Sapiens Madura is most likely the oldest Homo sapiens seen from phylogenetic trees. The results of this study are expected to be able to add Indonesia’s normal human database.

A revision of Onychelmis Hinton, 1941 (Coleoptera: Elmidae), with description of new species, DNA barcoding and notes on the geography of the genus

The genus Onychelmis Hinton, 1941 was for a long time regarded as a small taxon with only three known species distributed in the Andes. A study of new material from Ecuador, using morphological and molecular data, has resulted in the discovery of five new species: Onychelmis lenkae sp. nov., O. lobata sp. nov., O. minor sp. nov., O. onorei sp. nov. and O. splendida sp. nov. We also revised the entire genus and redescribed the three known species, O. longicollis (Sharp, 1882), O. leleupi Delève, 1968 and O. whiteheadi Spangler & Santiago, 1991. Habitus photographs of adults are provided, together with line drawings of male and female genitalia, and schematic illustrations of the distribution of femoral tomentum for each species. DNA sequences for barcoding the COI mtDNA fragment were used to support species delimitation and to suggest possible relationships among species. The revision includes a key to adults of all species of Onychelmis and notes on the biogeography of the genus, with an updated distribution map.

Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp (♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage.

Previously, a homodiploid goldfish-like fish (2n = 100; GF-L) was spontaneously generated by self-crossing a homodiploid red crucian carp-like fish (2n = 100; RCC-L), which was in turn produced via the distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) and male blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48). The phenotypes and genotypes of RCC-L and GF-L differed from those of the parental species but were similar to diploid red crucian carp (2n = 100; RCC) and goldfish (2n = 100; GF), respectively. We sequenced the complete mitochondrial DNAs (mtDNAs) of the KOC, BSB, RCC-L, GF-L, and subsequent generations produced by self-crossing [the self-mating offspring of RCC-L (RCC-L-F2) to the self-mating offspring of RCC-L-F2 (RCC-L-F3) and the self-mating offspring of GF-L (GF-L-F2)]. Paternal mtDNA fragments were stably embedded in the mtDNAs of both lineages, forming chimeric DNA fragments. In addition to these chimeras, several nucleotide positions in the RCC-L and GF-L lineages differed from the parental bases, and were instead identical with RCC and GF, respectively. Moreover, RCC-L and GF-L mtDNA organization and nucleotide composition were more similar to those of RCC and GF, respectively, compared to parental mtDNA. Finally, phylogenetic analyses indicated that RCC-L and GF-L clustered with RCC and GF, not with the parental species. The molecular dating time shows that the divergence time of KOC and GF was about 21.26 Mya [95% highest posterior density (HPD): 24.41–16.67 Mya], which fell within the period of recent. The heritable chimeric DNA fragments and mutant loci identified in the mtDNA of the RCC-L and GF-L lineages provided important evidence that hybridizations might lead to changes in the mtDNA and the subsequent generation of new lineages. Our findings also demonstrated for the first time that the paternal mtDNA was transmitted into the mtDNA of homodiploid lineages (RCC-L and GF-L), which provided evidence that paternal DNA plays a role in inherited mtDNA. These evolutionary analyses in mtDNA suggest that GF might have diverged from RCC after RCC diverged from koi carp.

Phylogeography and ecological niche modeling reveal evolutionary history of Leiolepis ocellata (Squamata, Leiolepidae).

Leiolepis ocellata is a lizard species distributing in topographically diverse habitats in northern Thailand. To explore its evolutionary history, 113 samples of L. ocellata were collected from 11 localities covering its distributional range in northern Thailand, and sequenced for mtDNA fragments (Cyt b and ND2). Pairwise comparisons across sampling localities yielded significant genetic differentiation (F ST and Jost's D) but no clear pattern of isolation by distance could be demonstrated based on the Mantel test. Phylogenetic and network analyses highlighted six haplogroups. Their divergence times were estimated to occur during the Pleistocene, much more recent than major orogenic events affecting northern Thailand. Instead, the results suggested that lineage divergences, of particularly eastern and western haplogroups of the region, coincided with the major rivers in the region (Yom river and Ping river, respectively), indicating vicariance in response to riverine barriers. Furthermore, ecological niche modeling suggested an expansion of suitable habitats of L. ocellata, when LGM‐liked conditions. This expansion potentially facilitated their dispersal among adjacent localities leading to lineage diversification and genetic admixture, after the riverine divergence.

Phylogeography, morphology and ecological niche modelling to explore the evolutionary history of Azure-crowned Hummingbird (Amazilia cyanocephala, Trochilidae) in Mesoamerica

The Pleistocene climate cycles and mountain uplift both affected the diversification of taxa in Mesoamerica. Yet, phylogeographic breaks and demographic responses of co-distributed taxa are not congruent. Investigation of more species with widespread distributions across Mexico and Central America will help shed light on how Earth historical events shaped biodiversity in this region. The Azure-crowned Hummingbird (Amazilia cyanocephala) is widely distributed from eastern Mexico into Central America and has been divided into three subspecies by morphology and geographic isolation. To investigate the evolutionary history of the species, we sequenced a non-coding mtDNA fragment along with a nuclear marker across its distribution, and analysed morphological and ecological variation and distributional projections derived from ecological niche modelling. Overall, mtDNA supported genetic differentiation among A. cyanocephala populations, which generally supports the existence of four lineages: two A. c. cyanocephala lineages separated by the Isthmus of Tehuantepec (east and west), A. c. guatemalensis populations separated by the Motagua-Polochic-Jocotan fault system, and the isolated A. c. chlorostephana in Honduras and Nicaragua. However, morphological data were not consistent with this phylogeographic result. The potential distribution of suitable habitat for A. cyanocephala was expanded during the Last Glacial Maximum and more contracted and fragmented during the Last Inter-Glacial and the Present. These models are consistent with a preglacial demographic expansion in A. c. cyanocephala. Mitochondrial genetic diversity and current precipitation seasonality were negatively correlated when analysing all populations. We suggest that isolation and habitat differences have both played a role in the recent diversification of A. cyanocephala. Inferences about the demographic consequences of isolation and subspecies recognition await further study.

Two new species of terrestrial-breeding frogs (Anura: Brachycephaloidea) from Cordillera de Colán, Peru

ABSTRACT We describe two new species of terrestrial-breeding frogs from the Cordillera de Colán, in northeastern Peru. We used Parsimony and Maximum Likelihood approaches to infer a molecular phylogeny on a dataset composed of 75 terminals, including three terminals representing the new species, and 4202 bp of concatenated mtDNA and nuDNA fragments. Our phylogenetic analyses support the placement of the two new species in Lynchius and Oreobates, respectively. The new species of Lynchius occurs in two localities from 1,977 to 2,006 m a.s.l., and is characterized by having a dorsum covered by conical tubercles and a brown dorsal coloration lacking a pattern of blotches on the hidden surfaces of flanks and hindlimbs. The new species of Oreobates is only known from one location at 2608 m a.s.l. and is characterized by the absence of axillary and inguinal glands, and the presence of white or cream blotches on the dark brown hidden surfaces of the body.

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This study represents the first molecular and morphological work on spiders of Iraq. Specimens were collected from different localities in seven provinces during June 2018-July 2019 in different climate conditions. Using both molecular and morphological approaches, eight families representing 17 genera and nine species were identified. Eight genera: Cryptachaea Archer, 1946; Micaria Western, 1851; Ozyptila Simon, 1864; Paramicromerys Millot, 1946; Tegenaria Latreille, 1804; Trachyzelotes Lohmander, 1944; Uroctea Dufour, 1820 and Zelotes Gistel, 1848; and five species: Cryptachaea riparia (Blackwall, 1834); Tegenaria pagana C. L. Koch, 1840; Trachyzelotes jaxartensis (Kroneberg, 1875); Pardosa amentata (Clerck, 1757) and Oecobius putus O. Pickard-Cambridge, 1876 were first recorded for the Iraqi spider fauna. Identification keys for distinguishing families and genera based on the main characteristics were constructed. Molecular-identification was performed for specimens that were difficult to identify by morphological methods, and to confirm the results of the morphological identification. DNA was extracted from 28 spiders’ specimens; PCR-amplified the mtDNA fragment of 710bp of the Cytochrome C Oxidase Subunit I (COI) gene using the primers LCO 1490 Forward / HCO-700ME Reverse. The results of DNA sequences showed 16 samples successful in sequencing. Sixteen local sequenced specimens were submitted to GenBank and edited and combined with COI gene sequences that are associated in GenBank using the neighbor-joining method and the phylogenetic tree was drawn. Eight species of 16 genera belonging to eight families were confirmed by molecular barcoding. The DNA sequences and associated information about the specimens (collection and locality date) deposited in GenBank.

Regional population genetics and global phylogeography of the endangered highly migratory shark Lamna nasus: Implications for fishery management and conservation

Abstract The porbeagle shark Lamna nasus is a large highly migratory shark distributed in cold and temperate marine waters of the North Atlantic and Southern Hemisphere (SH). According to the International Union for Conservation of Nature, the porbeagle is assessed globally as Vulnerable and regionally as Critically Endangered in the North Atlantic and the Mediterranean Sea. This study explored, for the first time, the population genetics of L. nasus at a regional (south‐east Pacific Ocean) and global scale. In this study, the null hypotheses of no genetic discontinuities among populations (i) within the SH, and (ii) between the SH and Northern Hemisphere (NH) were tested. Also, the demographic history of L. nasus in different ocean basins was assessed. Two mitochondrial markers (Control Region [CR] and cox1) well suited for population genetics inferences in sharks were used. Spatial–genetic analyses suggested two genetic clusters co‐occurring in the south‐eastern Pacific Ocean. A two‐way ANOVA using the cox1 but not the CR mtDNA fragment detected an effect of genetic identity on shark body size. Phylogeographic analyses, haplotype networks, and analyses of molecular variance demonstrated genetic differences between populations from the NH and SH but not among populations in the SH. Migration estimates indicated limited current maternal gene flow between the two hemispheres but high gene flow within hemispheres. Two well‐defined haplotype groups with star‐like shapes inhabited all ocean basins in the SH. These results could reflect a historical scenario of reproductive isolation and more recent mixture among previously isolated populations in the SH. A Bayesian skyline plot analysis indicated sudden population expansion in the SH occurring ~100–125 kya. This study highlights the need for additional studies focusing on the population genomics (using nuclear markers, i.e. single nucleotide polymorphisms) and the general biology of L. nasus to explore the existence of genetically dissimilar populations in the SH. Such studies will help implementing efficient genetic monitoring programmes.

Discovery of a Novel Mtdna Sequence in the Eastern Buzzard (Buteo Japonicus) in Japan

In recent years, several phylogenetic studies on the genus Buteo have been conducted. However, little is known about the lineage of the Eastern Buzzard (Buteo japonicus). We sequenced 919-bp fragments of mtDNA from 45 Eastern Buzzards from Japan and compared them with the sequences of the genus Buteo registered in the DDBJ/EMBL/GenBank databases. ND6 and pseudo control region phylogenetic analyses were performed on 15 and 35 specimens in the database, respectively. All 45 Eastern Buzzards from Japan possessed the same novel sequence in the ND6 gene, which differed in four base pairs from sequences previously reported for the Eastern Buzzard from continental Asia. Phylogenetic analysis of the ND6 gene showed that Japanese birds with the novel sequence did not form a clade with those from continental Asia with the previously reported sequences; instead, the continental Eastern Buzzard formed a clade with Himalayan Buzzards (Buteo refectus). A phylogenetic tree constructed using pseudo control region sequences showed that Eastern Buzzards were divided into two groups: one containing the Himalayan Buzzard, and one containing birds with the novel sequence. Our results suggested that the novel sequence revealed in this study is a geographic variant that may represent the “true” Eastern Buzzard, and that the previously reported sequence (from continental Asia) is that of the Himalayan Buzzard. We suggest that it is necessary to examine the habitats and characteristics of Eastern and Himalayan Buzzards in eastern Eurasia to more accurately classify these birds.

Heating histories and taphonomy of ancient fireplaces: A multi-proxy case study from the Upper Palaeolithic sequence of Abri Pataud (Les Eyzies-de-Tayac, France)

While the use of fire has long been recognised as a crucial innovation in the cultural evolution of humankind, much research has focused on the (debated) chronology of its earliest use and control, and less on the ways in which fire was used in the deep past. At its latest by the Upper Palaeolithic, hunter-gatherers routinely used fire to heat a wide range of materials, adjusting parameters like temperature, exposure time and fuel type to the specific requirements of the treated materials, for instance in food preparation or tool production.Comparing analyses of the chemical and physical properties of modern materials, heated under a range of controlled conditions in a laboratory, to archaeological ones might allow the reconstruction of the “heating history” of excavated materials and hence to infer the function of particular fires in the past - provided changes affecting the properties of the heated archaeological material during burial time are taken into consideration. To investigate the feasibility of such an approach, heated materials sampled from ~40,000 to 25,000 year old fireplaces (hearths) and their sedimentary matrices from the Upper Palaeolithic Abri Pataud rock shelter in South-Western France are used here to study (1) the fuel type(s) used by the site’s occupants, (2) the temperatures reached in fireplaces and (3) the potential changes in human activities related to fireplaces over time, with the influence of post-depositional processes taken into explicit consideration throughout. For this purpose, we used a range of methods to analyse macroscopically visible as well as “invisible” (microscopic and molecular) heat-altered materials.The results suggest that charred organic materials (COM) encountered in the samples predominantly result from the fuel used in fireplaces, including the earliest reported use of dung as fuel. Earlier suggestions about the use of bone as fuel at the Abri Pataud are not supported by this study. The heating temperature of COM increased gradually from 350 °C in the Aurignacian to 450 °C in Gravettian levels. Py-GC–MS studies identified a range of organic compounds, biomolecules derived from plant as well as animal sources, still preserved in the sediments after exposure to heat and burial in the rock shelter more than 20,000 years ago. Mammalian mtDNA was identified in sediment samples retrieved from the fireplaces, including ancient mtDNA fragments that originated from one or more modern human-like mitochondrial genome(s). This makes the Abri Pataud the first archaeological site for which ancient modern human mtDNA has been retrieved from sediment samples.The absence of specific organic compounds (furans) in the Aurignacian levels and their presence in the Gravettian ones, the changes in temperatures reached through the Aurignacian-Gravettian sequence as well as changes in the character of the fireplaces (presence/absence of lining river pebbles) suggest that the functions of hearths changed through time.These results highlight the potential of multi-proxy analyses of macro- and microscopic traces of ancient fireplaces, and especially of a shift in focus towards molecular traces of such activities. Systematic sampling of fireplaces and their sedimentary matrix should become a standard part of the excavation protocol of such features, to improve our understanding of the activities of humans in the deep past.

Pro-inflammatory role of cell-free mitochondrial DNA in cardiovascular diseases.

Cardiovascular disease (CVD) is a major cause of morbidity and mortality. Inflammation contributes to the pathogenesis and progression of CVD. Circulating cell-free mitochondrial DNA (ccf-mtDNA) is that mtDNA fragments are released outside the cell and into the circulation by cell necrosis and secretion. The levels of ccf-mtDNA are increased in CVD and associated risk conditions, including hypercholesterolemia, diabetes mellitus, and arterial hypertension. MtDNA containing unmethylated CpG dinucleotides and can trigger inflammation that aggravates tissue injury by activating toll-like receptor 9, inflammasomes, and the stimulator of interferon genes pathway. Here, we review the expanding field of ccf-mtDNA-mediated inflammation and its role in the progression of CVD.

Next generation sequencing-based analysis of mitochondrial DNA characteristics in plasma extracellular vesicles of patients with hepatocellular carcinoma.

Emerging evidence has revealed that mitochondrial DNA (mtDNA) is encapsulated in plasma extracellular vesicles (EVs). However, the characteristics of mtDNA in EVs from patients with cancer remain largely unexplored, which greatly limits its clinical application. Whole genome and capture-based sequencing found that EV mtDNA covered the whole mitochondrial genome. The medium fragment size in EV mtDNA was significantly larger compared with that in cell-free mtDNA [cfmtDNA; 159 vs. 109 base pairs (bp); P<0.001]. EV DNA appeared to have a higher mtDNA copy number compared with cfDNA. Of note, patients with hepatitis had >300-bp fragments in EV mtDNA compared with patients with hepatocellular carcinoma (HCC) and healthy controls. EV mtDNA fragments >300 bp in length exhibited a significantly higher proportion of EV mtDNA fragment ends than those that were ≤300 bp in length in patients with hepatitis. The EV mtDNA copy number in patients with HCC and hepatitis were significantly lower compared with those in healthy controls. Furthermore, inconsistencies in the mtDNA heteroplasmic variant were observed among HCC tissues, plasma and EVs. In conclusion, EV mtDNA exhibited different characteristics among patients with HCC, hepatitis and healthy controls, indicating the potential value of EV mtDNA as a diagnostic biomarker that complements cfmtDNA.

Assessing impact of dams on genetic diversity of native fish Mastacembelus armatus in river Yamuna using mitochondrial DNA cytochrome-b sequences as a molecular marker

Several dams have been constructed in Uttarakhand. In the present study an investigation on impact of dams on genetic diversity of native fish species Mastacembelus armatus at the Asan barrage on river Yamuna near Vikasnagar, Uttarakhand in India was done. Partial sequence of mitochondrial Cytochrome-b (Cyto-b) gene was used to determine the genetic variation in the population of Mastacembelus armatus. DNA was extracted from Mastacembelus armatus (n=33) samples, collected from river Yamuna and its tributary Asan from fin and fishes were released back in their habitat. Cytochrome c oxidase I (COI) was used to ascertain the species of fish along with morphometric characters. Analysis of 324 bp mtDNA fragment of Cyto-b revealed the presence of 06 haplotypes with nucleotide diversity, value ranged from 0.0172 to 0.0021 low pair wise Fst value was observed negative (-0.00125) when compared between Asan barrage and Kalsi site. No genetic subdivisions between the population were found after or before the dam sites. Tajima’s D value for river Asan, site A1 Mirzapur (before dam) was -0.1167 (a negative value). Negative Tajima D value can be indicative of recent selective sweep or population expansion after a recent bottleneck and linkage to a swept gene. Our data shows that fragmentation of habitat by dams does not have any impact on the genetic diversity of non-migrating Mastacembelus armatus fish species.

Patterns of mitochondrial DNA fragmentation in bread wheat (Triticum aestivum L.) seeds under ex situ genebank storage and artificial aging

Monitoring viability loss of seeds conserved ex situ for timely germplasm regeneration is a challenging task in germplasm management and conservation as the process of seed deterioration under long-term storage remains poorly understood and effective tools for assessing seed deterioration are lacking. This paper reports findings from four experiments that were aimed to study the fragmentation of mitochondrial DNA (mtDNA) due to degradation in naturally or artificially aged (NA or AA) wheat seeds. Together, it was found that mtDNA fragmentation occurred in aged wheat seeds. More mtDNA fragmentation was observed in AA than NA seeds and degradation was more prominent in abnormal seedling tissues than in normal seedling tissues. Fragmentation of mtDNA was linearly associated with sample germination; more in less viable seed samples. Mitochondria (mt) in aged seeds were found to break throughout the mitochondrial genome with the observed loss of PCR amplification of atp1-5, nad4.2, atp4, and nad9 gene loci and at the roughly 80 kb repetitive region. These findings are useful for understanding the process and involvement of mtDNA degradation in NA or AA wheat seeds and for further exploration to develop aging biomarkers for monitoring seed viability.

Genetic variation and phylogeographic structure of Spodoptera exigua in western China based on mitochondrial DNA and microsatellite markers.

The beet armyworm, Spodoptera exigua, is a significant agricultural pest of numerous crops and has caused serious economic losses in China. To effectively control this pest, we analyzed its genetic variation, population genetic structure and demographic history. We used mitochondrial DNA (mtDNA) fragments of the cytochrome oxidase subunit I (COI) and eight nuclear microsatellite loci to investigate genetic diversity and population genetic structure of S. exigua populations at 14 sampling sites in western China. Both mtDNA and microsatellite data indicated low levels of genetic diversity among all populations. A moderate genetic differentiation among some S. exigua populations was detected. Neighbor-joining dendrograms, STRUCTURE, and principal coordinate analysis (PCoA) revealed two genetically distinct groups: the KEL group and the remaining population group. Isolation by distance (IBD) results showed a weak significant correlation between geographic distance and genetic differentiation. Haplotype networks, neutrality testing, and mismatch distribution analysis indicated that the beet armyworm experienced a recent rapid expansion without a recent genetic bottleneck in western China. Thus, the results of this population genetic study can help with the development of strategies for managing this highly migratory pest.

Insertions of mitochondrial DNA into the nucleus-effects and role in cell evolution.

We review the insertion of mitochondrial DNA (mtDNA) fragments into nuclear DNA (NUMTS) as a general and ongoing process that has occurred many times during genome evolution. Fragments of mtDNA are generated during the lifetime of organisms in both somatic and germinal cells, by the production of reactive oxygen species in the mitochondria. The fragments are inserted into the nucleus during the double-strand breaks repair via the non-homologous end-joining machinery, followed by genomic instability, giving rise to the high variability observed in NUMT patterns among species, populations, or genotypes. Some de novo produced mtDNA insertions show harmful effects, being involved in human diseases, carcinogenesis, and ageing. NUMT generation is a non-stop process overpassing the Mendelian transmission. This parasitic property ensures their survival even against their harmful effects. The accumulation of mtDNA fragments mainly at pericentromeric and subtelomeric regions is important to understand the transmission and integration of NUMTs into the genomes. The possible effect of female meiotic drive for mtDNA insertions at centromeres remains to be studied. In spite of the harmful feature of NUMTs, they are important in cell evolution, representing a major source of genomic variation.

Diverse roles of mtDNA in schizophrenia: Implications in its pathophysiology and as biomarker for cognitive impairment

Schizophrenia (SZ) is a mental disorder characterized by neurocognitive dysfunctions and a reduction in occupational and social functioning. Several studies have provided evidence for mitochondrial dysfunction in the pathophysiology of SZ. In this sense, it is known that the addition of genetic variations in mitochondrial DNA (mtDNA) impairs oxidative phosphorylation of enzymatic complexes in mitochondria, resulting in ATP depletion and subsequent enhancement of reactive oxygen species; this is associated with cellular degeneration and apoptosis observed in some neuropsychiatric disorders. As a consequence of mitochondrial dysfunction, an increase in circulating cell-free mtDNA fragments can occur, which has been observed in individuals with SZ. Moreover, due to the bacterial origin of mitochondria, these cell-free mtDNA fragments in blood plasma may induce inflammatory and immunogenic responses, especially when their release is enhanced in specific disease conditions. However, the exact mechanism by which mtDNA could be released into blood plasma is not yet clear. Therefore, the aims of this review article were to discuss the participation of mtDNA genetic variations in physiopathologic mechanisms of SZ, and to determine the status of the disease and the possible ensuing changes over time by using circulating cell-free mtDNA fragments as a biomarker.

Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs

The Indian cheetah was hunted to extinction by the mid-20th century. While analysis of 139 bp of mitochondrial DNA (mtDNA) has confirmed that the Indian cheetah was part of the Asiatic subspecies (Acinonyx jubatus venaticus), the detailed relationships between cheetah populations remains unclear due to limited genetic data. We clarify these relationships by studying larger fragments of cheetah mtDNA, both from an Indian cheetah museum specimen and two African cheetah, one modern and one historic, imported into India at different times. Our results suggest that the most recent common ancestor of cheetah mtDNA is approximately twice as ancient as currently recognised. The Indian and Southeast African (Acinonyx jubatus jubatus) cheetah mtDNA diverged approximately 72 kya, while the Southeast and Northeast African (Acinonyx jubatus soemmeringii) cheetah mtDNA diverged around 139 kya. Additionally, the historic African cheetah sampled from India proved to have an A. j. jubatus haplotype, suggesting a hitherto unrecognised South African route of cheetah importation into India in the 19th century. Together, our results provide a deeper understanding of the relationships between cheetah subspecies, and have important implications for the conservation of A. j. venaticus and potential reintroduction of cheetahs into India.

Phylogeography and Mitochondrial Polymorphism of Asian Coho Salmon

Multiple Pleistocene glaciations significantly affected the gene pool of many species inhabiting the Northern part of the Pacific Rim, an area with a rich glacial history. This paper is devoted to the study of intraspecific polymorphism of the coho salmon and the routes of its settlement throughout the Asian part of its range. Such problems are traditionally solved by comparing parts of the mitochondrial genome. Here, two fragments of mtDNA, the control region (D-loop) and the cytochrome b gene (cytb), were investigated. It was shown that the settlement of the Asian Pacific coast by the coho salmon was preceded by a chain of successive migration events from the refugium located on the North American continent to the South of the ice sheet covering the area of modern Canada and southern Alaska. The low level of genetic polymorphism in Asian coho populations seems to be a result of a pronounced founder effect, rather than being characteristic of the species as a whole.

БИОИНФОРМАЦИОННЫЙ АНАЛИЗ НУКЛЕОТИДНЫХ ПОСЛЕДОВАТЕЛЬНОСТЕЙ ФРАГМЕНТА ГЕНА ЦИТОХРОМОКСИДАЗА МТДНК ПАЛТУСОВ (PLEURONECTIDAE)

Comparative bioinformation analysis of nucleotide composition of subunit 1 cytochrome oxydase gene (Co-1) mtDNA subunit of north-okhotomore population with representatives of other halibut genera was carried out. Statistical analysis of nucleotide sequences of a fragment of the gene cytochrome oxidase mtDNA of pacific halibut Hippoglossus stenolepis: haplotype diversity 0.852 ± 0.0059, nucleotide 0.00430 ± 0.009465. About 1% of the total value of nucleotide diversity in individuals from eastern and western regions is determined. Analysis of nucleotide sequences of the same gene in pacific greenland halibut Reinhardtius hippoglossoides matsuurae: haplotype diversity was 0.806 ± 0.0399, nucleotide diversity - 0.00185 ± 0.000149. About 6% of the relative value of nucleotide diversity is determined by interpopulation differences. The minimum value of haplotype diversity was determined in the northern halibut flounder Hippoglossus robustus, while in the second species of this genus Hipploglossus platessoides, the haplotype diversity is similar to the representatives of two genera Cleisthenes and Hippoglossus. The maximum value of haplotypic diversity was found in the Cleisthenes herzensteini, representatives of the Atherestes and Reinchardtius genera have intermediate values. The species Atherestes stomias is sharply separated from species of other genera, which is associated with a high degree of genetic differences between representatives of this genus and those from other genera.