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22 results for “Cyt b”
Brook trout (Salvelinus fontinalis) cyt b qPCR data from Hidden Lake (Banff National Park, Canada) over two rotenone applications between 2018 and 2020.
Water samples were taken in Hidden Lake at five different time points around two rotenone applications: (i) five weeks prior to the first rotenone application, on July 12 2018; (ii) approximately three weeks after the first application of rotenone, on 7 September 2018; (iii) approximately 10 months after the first rotenone application, on 10 July 2019; and (iv) one year after the final rotenone treatment, on 19 August 2020. For each time point, four pelagic and four littoral water samples were taken from Hidden Lake, as well as 8 to 13 water samples from Hidden Creek and Coral Creek for a total of 16 to 21 samples per time point. Quantitative PCR (qPCR) method was used to produce brook trout (Salvelinus fontinalis) cytochrome b copy number for each sample. The objective of this study was use eDNA to assess the efficacy of invasive brook trout removal using rotenone.
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)
FIGURE 4. Combined cyt-b and D in Systematics and Taxonomy of Great Striped-Faced Bats of the Genus Vampyrodes Thomas, 1900 (Chiroptera: Phyllostomidae)
FIGURE 4. Combined cyt-b and D-loop maximum likelihood phylogram for both species of Vampyrodes. Support statistics from a parsimony bootstrap analysis, a maximum likelihood bootstrap analysis, and a Bayesian analysis are indicated at each resolved node. For the parsimony and maximum likehood analyses (MP and ML, respectively), white indicates bootstrap frequencies ≤50%, grey indicates bootstrap frequencies between 50% and 75%, and black indicates bootstrap frequencies ≥75%. For the Bayesian analysis (BPP), white indicates posterior probabilities <0.95, whereas black indicates posterior probabilities ≥0.95. For each terminal, an alphanumeric identifier and the country of origin (from table 1). Numbers in parentheses refer to localities mapped in figure 6 and listed in the Gazetteer (appendix).
FIGURE 5. Cyt b in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 5. Cyt b tree for Monitilorinae and Lucininae, expanded from Figure 4.
DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
<p>As an island endemic with a decreasing population, the Critically Endangered Grenada Dove <em>Leptotila wellsi</em> is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (<em>ND2</em>) and Cytochrome b (<em>Cyt b</em>). Haplotype diversity (<em>h</em>) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the <em>ND2</em> sequences; a single haplotype was identified within the <em>Cyt b </em>sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potential augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species. </p>
DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
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FIGURE 1. Bayesian inference tree derived from the cyt b in Vanmanenia intermedia Fang, 1935, a valid hill-stream species of loach (Teleostei Gastromyzontidae) from the middle Yangtze River basin, Southwest China
FIGURE 1. Bayesian inference tree derived from the cyt b gene for nine species of Vanmanenia. Nodal numbers are posterior probability values larger than 50%.
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013). in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013).
FIGURE 1. Bayesian tree derived from cyt b in Invalidity of Hynobius yunanicus and molecular phylogeny of Hynobius salamander from continental China (Urodela, Hynobiidae)
FIGURE 1. Bayesian tree derived from cyt b data for hynobiid salamanders (sample number at the top of species name). Onychodactylus japonicus was used as outgroup. Nodal values indicate Bayesian posterior probability and bootstrap supports for ML inferences (1000 replicates). Numbers in shaded circles show samples from China.
FIGURE 4. Bayesian inference tree derived from cyt b in Molecular evidence for taxonomic status of the gudgeon genus Huigobio Fang, 1938 (Teleostei: Cypriniformes), with a description of a new species from Guangdong Province, South China
FIGURE 4. Bayesian inference tree derived from cyt b gene for the Armatogobionina of the subfamily Gobioninae. Nodal numbers are posterior probability values. Only values above 50% are given.
FIGURE 2. Maximum Likelihood tree for cyt b in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 2. Maximum Likelihood tree for cyt b haplotypes (1060 bp) of Rhinoclemmys melanosterna, including sequences of the other eight Rhinoclemmys species. Haplotype codes correspond to Figure 3 and Appendix I (see there for GenBank accession numbers). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities> 0.95 in Bayesian analyses. Root length shortened by 75%. Note the polyphyly of R. melanosterna.
Fig. 4. Minimum spanning network and mismatch distribution from cyt b in Echinoderes galadrielae Grzelak & Sørensen 2022, sp. nov.
Fig. 4. Minimum spanning network and mismatch distribution from cyt b DNA sequences of Rhodeus ocellatus in each lineage. The colors correspond to the lineage in figure 2. The size of each circle represents the number of specimens of each haplotype. The small, open circle between different haplotypes represents the number of mutations. The number of mutations> 8 is shown as the mutation number beside the traverse lines. The results of mismatch distribution are shown in the histograms. The abscissa and ordinate of the histograms indicate the number of pairwise difference between specimens and the frequency of each value, respectively. The black and gray bars represent the frequency distribution of the observed and expected pairwise difference respectively under the sudden expansion model.
Fig. 5. Demographic inference from cyt b in Echinoderes galadrielae Grzelak & Sørensen 2022, sp. nov.
Fig. 5. Demographic inference from cyt b sequences of Rhodeus ocellatus in East Asia. (A) Mismatch distribution of total population. The abscissa and ordinate of the histograms indicate the number of pairwise difference between specimens and the frequency of each value, respectively. The black and gray bars represent the frequency distribution of the observed and expected pairwise difference respectively under the sudden expansion model. (B) Bayesian skyline plot (BSP) of total population estimated by 1.05% per site per million year of evolutionary rate. The black line indicates the mean curve of BSP. The dotted line indicates the 95% highest posterior density intervals of the BSP. The x-axis indicates the time (million years ago, mya). The y-axis is the estimated effective population size.
FIGURE 1. Condensed Bayesian tree inferred from cyt b in Capoeta anamisensis, a new species from the Minab and Hasan Langhi River drainages in Iran (Teleostei: Cyprinidae)
FIGURE 1. Condensed Bayesian tree inferred from cyt b. Numbers right of the slash, indicate the posterior probabilities of the Bayesian analysis, using MrBayes, while numbers left of the slash are the bootstrap support for 10,000 replicates in the Maximum Likelihood tree, using RaxML. Asterisks (*) indicate less than 50% Maximum Likelihood support for the node.
FIGURE 1. Phylogenetic tree for Cyt b in A phylogenetic assessment of the meadow lizard Darevskia praticola (Eversmann, 1834) from Iran
FIGURE 1. Phylogenetic tree for Cyt b gene, aS BayeSian and ML analySeS Show Similar tree topologieS only the ML tree iS preSented. NumberS on brancheS are bootStrap Support valueS for ML (below) and poSterior probability valueS for BayeSian (above) analySeS. Only valueS greater than 70 and 0.7, reSpectively, are Shown
FIGURE 4. Unrooted Cyt b in Revision of the genus Leopoldamys (Rodentia, Muridae) as inferred from morphological and molecular data, with a special emphasis on the species composition in continental Indochina
FIGURE 4. Unrooted Cyt b ML tree showing the Leopoldamys genetic lineages radiation. The external root position as indicated by arrow.
FIGURE 3a. Bayesian phylogeny inferred from cyt b in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 3a. Bayesian phylogeny inferred from cyt b sequences partitioned by codon position for 34 East African specimens of O. typus s.l. and O. tropicalis s.l. in relation to representatives of seven Otomys species and Parotomys brantsii from eastern, western and southern Africa. Representatives of nine murine taxa served as outgroups (see Appendix 1). Nodal support indices for the main clades (annotated 1 to 8) and subclades (a, b, c, d and e), as well as supported deeper nodes (A, H, I, M, N, O) are given beside the phylogram in the following order: Bayesian posterior probabilities (BPP)/ bootstrap support from 1000 replicates for maximum likelihood (MLbs), under an unpartitioned GTR+I+G model/ unweighted parsimony (UwPbs), six-parameter-weighted parsimony partitioned by codon positions (6PPbs)/ neighbour-joining using uncorrected p-distances (Njpbs)/ neighbour-joining using GTR+I+G-corrected distances (Njcbs). Estimated divergence dates (Myr) for the major lineages identified in the cyt b phylogeny are indicated to the left of each node. Bayesian estimation of divergence times was conducted under a relaxed clock model using BEAST v.1.4. Four well established murine fossil calibration points were specified (Pocock 1987; Rowe et al. 2008, see text).
FIGURE 3b. Maximum likelihood phylogram constructed from combined cyt b and 12S rRNA sequences for 20 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 3b. Maximum likelihood phylogram constructed from combined cyt b and 12S rRNA sequences for 20 Otomys specimens, one representative of Parotomys brantsii and four murine outgroups under the best-fit GTR+I+G model. Support indices for each node (1 – 23) are given beside the phylogram (BPP/ MLbs/ UwPbs/ 6PPbs/ NJpbs/ Njcbs). For both phylogenies (Figure 3a and 3b), the relative branch thickness indicates significant nodal support from the phylogenetic reconstruction methods employed herein (four to six methods—thick lines; two methods—intermediate lines). Dashed lines show unsupported relationships; Abbreviations and symbols: NS - BPP <0.95; "-" indicates that the node was not present in the relevant analysis, or percentage bootstrap support below 50%.
FIGURE 2. Phylogenetic tree concluded using Cyt b in A new species of Acanthodactylus Fitzinger, 1834 (Sauria: Lacertidae) from the Zagros Mountains, Iran
FIGURE 2. Phylogenetic tree concluded using Cyt b gene for Acanthodactylus species. The topologies of BI and ML trees are the same, therefore only the ML tree is shown. Numbers on branches indicate posterior probabilities (above) and bootstrap supports (below). Only values greater than 0.9 (for the former) and 90 (for the latter) are shown.
FIGURE 5. Cyt b in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 5. Cyt b tree for Monitilorinae and Lucininae, expanded from Figure 4.
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