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42 results for “mtDNA sequence”
Figure 2. D in Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to an earthworm type, with a response to the 'Can of Worms' theory of cryptic species
Figure 2. D. hattamimizu unscaled habitus (from Watanabe, 2005, fig. 1 after Hatai's 1931 original).
Figure 7 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 7. Summary of Random Forests classifications for each empirical comparison. Each row shows results from the stratum with the smallest fraction of individuals correctly classified, with comparisons labeled by their taxonomic codes as listed in Table 2. Colors identify comparison type as species (blue), subspecies (green), and populations (red). Points show the fraction of individuals correctly classified with probabilities> 50% (PD50, circles), and> 95% (PD95, triangles). Thin colored lines show 95% confidence intervals (CI) around PD50 estimates. Gray bars show range of a priori random classification rates based on individual size (left) to maximum possible classification rates based on shared haplotypes (right).
Figure 6 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 6. Frequency distributions of the change in observed diagnosability (x-axis) in the simulated data for increasing levels of the probability of misstratification (vertical panels). Figures on the left and right columns are censored by data sets for original diagnosability ≤50% and>50%, respectively.
Figure 5 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 5. Two-dimensional GAM fits of theta (Ɵ), number of migrants (Nem), and divergence time in generations (T) from Model 2 simulated data. From left to right, columns show results from models without migration (m = 0), with migration and Nem <1, and Nem ≥ 1. Colors indicate model prediction of percent correctly classified.
Figure 4 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 4. GAM fit of number of migrants (Nem) from Model 2 parameters. Solid line shows median value of predicted percent correctly classified, and shaded area shows 95% CI. The switch from bimodal distribution to a normal distribution occurs at Nem = 1 (log10Nem = 0).
Figure 3 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 3. Two-dimensional GAM fits of effective population size (Ne), divergence time in generations (T), and mutation rate (µ) from Model 1 simulated data. Results from models without migration to the left and those with migration to the right. Colors indicate model prediction of percent correctly classified.
Figure 1 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 1. (A) Distribution of a hypothetical character for two putative subspecies (red and blue) demonstrating minimum overlap necessary to satisfy 75% rule of Amadon (1949). Character is continuous on the x-axis. Dashed lines indicate the point at which 75% of each distribution is outside of 99%+ of the other. Solid line indicates point of overlap where 97% of both distributions are outside one another. (B) Probability of membership to subspecies for specimens having values along the character axis. Probability is based on the ratio of the distribution frequencies at each point along the x-axis, with a 50:50 probability occurring at the threshold point.
Fig. 3. Phylogenetic trees from reported 18S in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig. 3. Phylogenetic trees from reported 18S rRNA genes of insects according to NJ. A. Based on sequences of full-length. B. Based on second conserved region.
Fig. 4 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig. 4. Phylogenetic trees based on partial sequences from reported cox1 genes of insects according to NJ.
Fig.1 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig.1. PCR result of 18S rRNA of Lymantria dispar. Separated bands (from left to right). 18S1, 18S2, 18S rRNA, DL2000 marker.
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019) in Variability of the gene cyt b in the Korean field mouse Apodemus peninsulae Thomas, 1906 - a reservoir host of AMRV in the Khasansky District of Primorsky Krai
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019)
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp). in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp).
Text-fig. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114. in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114.
Figure 2 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 2. Illustration of steps in constructing a Random Forests ensemble of classification trees.
MinION sequencing data of mtDNA from BH10 cells
<p><span>Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic because of its uniparental inheritance and subsequent homoplasmic state, which excludes the biological need for genetic recombination, as well as limits tools to study it. However, molecular recombination is an important genome maintenance mechanism for all organisms, most notably being required for double-strand break repair. To demonstrate the existence of mtDNA recombination, we have taken advantage of a cell model with two different types of mitochondrial genomes and impaired ability to turn over broken mtDNA. The resulting excess of linear DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA complexes and recombinant mtDNA genomes, detectable by Southern blot. Combining our observations with previously published work, we propose that the mitochondrial replisome can catalyze microhomology-mediated recombination of linear mtDNA ends, thus rendering a specialized mitochondrial recombinase unnecessary. The error-proneness of this system is likely to contribute to the formation of pathological mtDNA rearrangements.</span></p>
Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals
<p><span>Narrow-headed vole, together with collared lemming and common vole, was the most abundant small mammal species across Eurasian Late Pleistocene steppe-tundra environments. Previous ancient DNA studies of </span><span>the latter</span><span> </span><span>two</span><span> revealed dynamic past population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary </span><span>histories,</span><span> we generated a dataset comprising mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from multiple sites across Europe and north-</span><span>western</span><span> Asia and covering the last ca. 100 thousand years (ka). We inferred Bayesian time-aware phylogenies using 11 </span><span>radiocarbon-dated</span><span> samples for calibration of the molecular clock. We found that across the three </span><span>species,</span><span> divergence of the main mtDNA lineages occurred during Marine Isotope Stages (MIS) 7 and MIS 5, suggesting a common response </span><span>of species adapted to open habitat to the interglacial environments. </span><span>In European narrow-headed voles, we identified multiple </span><span>time-structured</span><span> mtDNA lineages, implying lineage turnovers. Timing of some of these turnovers was synchronous across all three </span><span>species,</span><span> allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.</span></p>
Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA
<p><span>Assigning prehistoric objects to specific individuals is usually impossible outside of burial contexts. Here we present a non-destructive method for gradually releasing DNA from ancient bone and tooth artifacts. Application of the method to an Upper Paleolithic deer tooth pendant from Denisova Cave (Russia) resulted in the recovery of DNA from both the deer and a female human individual. Genetic dates obtained from the deer and human mitochondrial genomes estimate the age of the pendant at approximately 20,000 to 24,000 years. Nuclear DNA from its presumed maker or wearer shows strong affinities to contemporaneous Ancient North Eurasian individuals previously found further east in Siberia. Our work opens up new possibilities for linking cultural and genetic records in prehistoric archaeology.</span></p>
Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA
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MinION sequencing data of mtDNA from BH10 cells
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Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals
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