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26 results for “cytochrome b sequence”
Cichlasoma urophthalmus cytochrome b sequences collected from the Florida Everglades (FCE) and Central America from January 2012 to May 2014
Cytochrome b sequences obtained from samples of Cichlasoma urophthalmus collected within the Florida Everglades and Central America. Samples were collected from fin clippings of fish caught by angling and/or cast netting. DNA was extracted, amplified and cytochrome b was sequenced. Data were used to determine the source for Mayan Cichlids in Florida.
Fig. 2 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences
Fig. 2. The neighbour-joining (A) and Bayesian (B) trees for Suncus inferred from 1140 base-pairs of cytochrome b gene sequence. Bootstrap and posterior probability values are given above branches.
Fig. 1 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences
Fig. 1. Male Malayan pygmy shrew (Suncus malayanus) captured in the Cameron Highlands, Pahang, Peninsular Malaysia, in a pitfall trap set on the forest floor. Notice the characteristic large ears and dark fine pelage.
Fig. 1. Collectionsitesfor 91 specimensfrom 29 locationsof Apodemusagrarius, usedin thisstudy. ThespecimennumberforeachlocationarelistedinTable 1 in Comparative Genetics Of Apodemus Agrarius (Rodentia: Mammalia) From Insular And Continental Eurasian Populations: Cytochrome B Sequence Analyses
Fig. 1. Collectionsitesfor 91 specimensfrom 29 locationsof Apodemusagrarius, usedin thisstudy. ThespecimennumberforeachlocationarelistedinTable 1, andminimum Jukes-Cantordistancesbetween 17 haplotypesfrommainlandKoreaandother 49 haplo- typesfromsevenregions (Taiwan, Jeju, northeasternChina, easternChina, centralChina, Far-easternRussia, andEurope) basedonthecytochrome b completesequencesaregiven
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 3 in Analysis of mitochondrial cytochrome b gene sequences of marine leech, Pterobdella arugamensis
Figure 3. Haplotype network of P. arugamensis CYTB gene sequences. Different colours represent different locations. The circle size is proportional to the sample number. Each dash on the line symbolises one mutational event. Tiny white circle indicates median vector.
Figure 2 in Analysis of mitochondrial cytochrome b gene sequences of marine leech, Pterobdella arugamensis
Figure 2. Representative maximum-likelihood tree showing nine haplotypes of P. arugamensis based on CYTB gene sequences. Ozobranchus jantseanus and Erpobdella japonica from the GenBank database were used as outgroups. The bootstrap percentages (1000 replicates) for maximum likelihood/maximum parsimony/neighbour joining trees are shown.
Figure 1 in Analysis of mitochondrial cytochrome b gene sequences of marine leech, Pterobdella arugamensis
Figure 1. Locations of P. arugamensis used in this study. Sampling locations are shown by blue circles: Brunei (TP: Tanjong Pelumpong, PK: Pulau Kaingaran), Surabaya in Indonesia (EJ), and Lombok in Indonesia (EL). Red circle indicates the GenBank sample from Hainan, China. The map was adapted from the USGS National Map Viewer (open access) at http://viewer.nationalmap.gov/viewer/.
Figure 2 in Investigation of genetic variation among Turkish populations of Andricus lignicola using mitochondrial cytochrome b gene sequence data
Figure 2. Bayesian analysis tree. Posterior probability values are given on the branches. Outgroup haplotypes: Ac (Andricus caliciformis) and Ak (Andricus kollari).
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records
Distribution. Until recently considered to occur in C & NE Angola and S & SE DR Congo, but based on cytochrome-b sequences, Bryja and colleagues in 2014 extended the range to include the NW region and the Eastern Arc Mts of Tanzania, much of NE Zambia, and Malawi; also re- corded from a single locality in extreme NW Zambia. in Muridae
Distribution. Until recently considered to occur in C & NE Angola and S & SE DR Congo, but based on cytochrome-b sequences, Bryja and colleagues in 2014 extended the range to include the NW region and the Eastern Arc Mts of Tanzania, much of NE Zambia, and Malawi; also re- corded from a single locality in extreme NW Zambia.
Figure 5 in Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome b sequences
Figure 5: Maximum likelihood tree of Suncus cytb sequences. Phylogenetic relationships inferred from a matrix of 1,140 nucleotide positions for 36 individuals. Maximum likelihood bootstrap supports above 50% and Bayesian posterior probabilities above 0.70 are indicated near the corresponding node separated with a slash. Sequences obtained in this work are indicated in bold. Authors of sequence data in Supplementary Table S6.
Figure 4 in Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome b sequences
Figure 4: Maximum likelihood tree of Crocidura suaveolens complex cytb sequences. Phylogenetic relationships inferred from a matrix of 996 nucleotide positions for 215 individuals. Maximum likelihood bootstrap supports above 50% and Bayesian posterior probabilities above 0.70 are indicated near the corresponding node separated with a slash. Sequences obtained in this work are indicated in bold. Authors of sequence data in Supplementary Table S5.
Figure 3 in Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome b sequences
Figure 3: Maximum likelihood tree of Crocidura leucodon cytb sequences. Phylogenetic relationships inferred from a matrix of 1,077 nucleotide positions for 63 individuals. Maximum likelihood bootstrap supports above 50% and Bayesian posterior probabilities above 0.70 are indicated near the corresponding node separated with a slash. Sequences obtained in this work are indicated in bold. Authors of sequence data in Supplementary Table S4.
Figure 2 in Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome b sequences
Figure 2: Maximum likelihood tree of Crocidura cytb sequences with emphasis on the Asian and Old World species. Phylogenetic relationships inferred from a matrix of 1,128 nucleotide positions for 131 individuals. Maximum likelihood bootstrap supports above 50% and Bayesian posterior probabilities above 0.70 are indicated near the corresponding node separated with a slash. Sequences obtained in this work are indicated in bold. Authors of sequence data in Supplementary Table S3.
Figure 1 in Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome b sequences
Figure 1: Shrew sample locations. A. samples sequenced in this work. B. shrew specimen present in the Steinhardt National Collection of Natural History, Zoological Museum at Tel Aviv University (Israel). The two major biomes of Israel: the Mediterranean biome, and the desert, are indicated in green and yellow, respectively. Red squares, blues stars, green circles and black triangles indicate C. ramona, S. etruscus, C. suaveolens gueldenstaedtii and C. leucodon specimen respectively. The museum records encompass 79 C. leucodon, 594 C. suaveolens gueldenstaedtii, 13 C. ramona and 443 S. etruscus.
Figure 2 from: Grzywacz B, Tatsuta H (2017) Phylogenetic relationship of Japanese Podismini species (Orthoptera: Acrididae: Melanoplinae) inferred from a partial sequence of cytochrome c oxidase subunit I gene. Journal of Orthoptera Research 26: 11-19. https://doi.org/10.3897/jor.26.14547
Figure 2 - Phylogenetic tree of Podismini based on the Bayesian analysis (BI) of concatenated COI sequences. BI posterior probability (PP) and maximum likelihood bootstrap values (BV) are shown near resolved branches (only support values above 50% are shown) as PP/BV. The respective clades are marked with a square and Roman numeral. We examined Ognevia longipennis from China because of the availability and thus did not treat this specimen as Japanese Podismini (see also text). Light green frames denote the Japanese Podismini analyzed in the present study.
Figure 2 from: Grzywacz B, Tatsuta H (2017) Phylogenetic relationship of Japanese Podismini species (Orthoptera: Acrididae: Melanoplinae) inferred from a partial sequence of cytochrome c oxidase subunit I gene. Journal of Orthoptera Research 26: 11-19. https://doi.org/10.3897/jor.26.14547
Figure 2 - Phylogenetic tree of Podismini based on the Bayesian analysis (BI) of concatenated COI sequences. BI posterior probability (PP) and maximum likelihood bootstrap values (BV) are shown near resolved branches (only support values above 50% are shown) as PP/BV. The respective clades are marked with a square and Roman numeral. We examined Ognevia longipennis from China because of the availability and thus did not treat this specimen as Japanese Podismini (see also text). Light green frames denote the Japanese Podismini analyzed in the present study.
Figure 3. Bayesian phylogram for cytochrome b sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D in Extensive diversification of pebblesnails (Lithoglyphidae: Fluminicola) in the upper Sacramento River basin, northwestern USA
Figure 3. Bayesian phylogram for cytochrome b sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D. Posterior probability values ≥ 90% are shown. Upper Sacramento River basin lineages newly discovered in this study are highlighted by the larger font. Specimen codes are from Table 1.
Figure 3 from: Md Zain B, Muhammad Abu Bakar A, Ruslin F, vui fui v, Abu M, Japning J, Abdul-Patah p, lakim m, Roos C, Yaakop S (2014) Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences. ZooKeys 407: 121-139. https://doi.org/10.3897/zookeys.407.6982
Figure 3 - Neighbor joining phylogenetic tree using Kimura-2-Parameter algorithm with bootstrap values indicated on the branch.
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