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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.
Figure 3. Consensus tree for the cytochrome b in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 3. Consensus tree for the cytochrome b dataset for representative genotyped specimens of the Rhinolophus hildebrandtii complex. The topology represents the consensus topology from a 20 million MCMC run implemented in BEAST. Estimates of divergence times (million years ago; Mya) are indicated adjacent to nodes or above branches and grey bars indicate 95% HPD values. The split between the Hipposideridae and Rhinolophidae was used as the calibration point. Taxa names include museum/field numbers which correspond to Appendix S1 or GenBank accession numbers and abbreviations are: RcfH - R. cf. hildebrandtiiı RD - R. darlingiı RE - R. eloquensı RF - R. fumigatusı RH - R. hildebrandtii s.l.ı RL - R. landeri and RR - R. ruwenzorii. Localitiesı where availableı are providedı abbreviations include SA - South Africaı MZ - Mozambiqueı and ZW - Zimbabweı and the numbers in parentheses correspond with place names in Table S1 and Fig. 2 for Clade 1 and 2 individuals. doi:10.1371/journal.pone.0041744.g003
Fig. 11. Bayesian inference trees. A. 16S rRNA dataset. B. Cytochrome oxidase I in Designation of a neotype for Myxicola infundibulum (Montagu, 1808) (Annelida: Sabellidae) and a new species from the UK
Fig. 11. Bayesian inference trees. A. 16S rRNA dataset. B. Cytochrome oxidase I gene dataset. The first value at each node represents maximum likelihood bootstrap support, the second the Bayesian posterior probabilities and the third the maximum parsimony bootstrap support.
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. 2. Minimum spanning network for haematozoa mitochondrial DNA cytochrome b in Prevalence and genetic diversity of haematozoa in South American waterfowl and evidence for intercontinental redistribution of parasites by migratory birds
Fig. 2. Minimum spanning network for haematozoa mitochondrial DNA cytochrome b haplotypes detected in South American waterfowl. Shaded circles represent unsampled nodes. All circles are drawn proportional to the frequency at which haplotypes were observed. Lines separating nodes are drawn to scale based on the number of nucleotide mutations, unless otherwise indicated by hash marks. Only haplotypes with a length of 358 bp or greater were included. Haplotype name abbreviations are as follows: Haem = Haemoproteus, Leuc = Leucocytozoon, and Plas = Plasmodium.
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
Figure 3. Phylogenetic tree inferred from cytochrome B in Phlebotomus (Paraphlebotomus) chabaudi and Phlebotomus riouxi: closely related species or synonyms?
Figure 3. Phylogenetic tree inferred from cytochrome B data of Phlebotomus chabaudi and Ph. riouxi specimens. We added to the analysis the sequences of Ph. chabaudi published by Tabbabi et al. (2014). The phylogram results from bootstrapped data sets obtained using the PhyML 3.0 program [21] using GTR (general time reversible) + G distribution (gamma distribution of rates with four rate categories). The tree was visualized using the TreeDyn program, version 198.3 [7]. The percentages above the branches are the frequencies with which a given branch appeared in 500 bootstrap replications. Only bootstrap values higher than 50% on the early branches are shown. A sequence of Ph. sergenti (AF161216) was used as the outgroup. The sequences marked by * were published by Tabbabi et al. (2014); R = sequences found in specimens morphologically characterized as Ph. riouxi. C = sequences found in specimens morphologically characterized as Ph. chabaudi. RC = sequences found in specimens morphologically characterized as Ph. chabaudi or Ph. riouxi. Int = sequences found in specimens morphologically characterized as intermediate between Ph. riouxi and Ph. chabaudi.
Fig. 3. Minimum spanning network for Haemoproteus and Plasmodium mitochondrial DNA cytochrome b in Spatial, temporal, molecular, and intraspecific differences of haemoparasite infection and relevant selected physiological parameters of wild birds in Georgia, USA
Fig. 3. Minimum spanning network for Haemoproteus and Plasmodium mitochondrial DNA cytochrome b haplotypes detected in four species of passerines from Georgia (USA). Circles are drawn proportional to the frequency at which haplotypes were observed. Color represents the host species from which haplotypes originated: red for Northern Cardinal (Cardinalis cardinalis), blue for Indigo Bunting (Passerina cyanea), yellow for White-throated Sparrow (Zonotrichia albicollis), and grey for Tufted Titmouse (Baeolophus bicolor). A single mutation separates nodes unless explicitly indicated by number. Letters within each node refer to Table 8 which indicates the haplotype name, sampling location, and other factors associated with hosts.
Fig. 4. Minimum spanning network for hematozoa mitochondrial DNA cytochrome b in Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California
Fig. 4. Minimum spanning network for hematozoa mitochondrial DNA cytochrome b haplotypes detected in Central Valley northern pintails. Circles are drawn proportional to the frequency at which haplotypes were observed. Shading represents the sample collection from which haplotypes originated: white (2006– 2007 wing muscle), grey (2011–2012 wing muscle), and black (2011–2012 blood). A single mutation separates nodes unless explicitly indicated by number. Lines separating nodes are drawn to scale unless indicated by a break. Parasite taxa have been abbreviated in haplotype names (Leu = Leucocytozoon, Hae = Haemoproteus and Pla = Plasmodium).
Fig. 1. Bayesian phylogenetic tree constructed using partial cytochrome b in Unexpected absence of exo-erythrocytic merogony during high gametocytaemia in two species of Haemoproteus (Haemosporida: Haemoproteidae), including description of Haemoproteus angustus n. sp. (lineage hCWT7) and a report of previously unknown residual bodies during in vitro gametogenesis
Fig. 1. Bayesian phylogenetic tree constructed using partial cytochrome b sequences of 61 lineages of Haemoproteus, 4 lineages of Plasmodium, and Leucocytozoon sp. lSISKIN2 as outgroup. Posterior probabilities higher than 0.8 are indicated close to the respective nodes. Red font indicates the parasite lineage described in this publication. Vertical bars (A–D) show groups of closely related lineages, which complete development and produce gametocytes only in non-passerines (A, D), both non-passerines and passerines (B), and only passerines (C). Blue font indicates Haemoproteus species, which develop in non-passerine avian hosts, which are indicated by symbols (● – Psittaciformes; ∎ - Coraciiformes; ▴ - Strigiformes; ◆ - Anseriformes; ★ - Charadriiformes; ♥ - Pelecaniformes; ⋄ - Piciformes; ⊠ - Sphenisciformes; Ω - Musophagiformes; § - Trochiliformes; Ψ – Falconiformes; Σ – Columbiformes; Φ - Galliformes). Lineage names were provided (according to MalAvi database), followed by parasite species names and sequence GenBank accession numbers.
Fig. 2. Minimum spanning network for haemosporidian mtDNA cytochrome b in Haemosporidian parasite infections in grouse and ptarmigan: Prevalence and genetic diversity of blood parasites in resident Alaskan birds
Fig. 2. Minimum spanning network for haemosporidian mtDNA cytochrome b haplotypes isolated from Alaskan grouse and ptarmigan species. Dark circles represent un-sampled nodes. All circles are proportional to the frequency at which the haplotypes were detected. Lines between nodes are drawn to scale based on the number of nucleotide mutations unless otherwise indicated by hash marks.
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).
Fig. 5. Phylogenetic tree depicting inferred genetic relationships among Leucocytozoon mitochondrial DNA cytochrome b in Negligible evidence for detrimental effects of Leucocytozoon infections among Emperor Geese (Anser canagicus) breeding on the Yukon-Kuskokwim Delta, Alaska
Fig. 5. Phylogenetic tree depicting inferred genetic relationships among Leucocytozoon mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the Yukon-Kuskokwim Delta, Alaska during 2006–2016 and those previously reported for closely related haemosporidian morphospecies on the National Center for Biotechnology Information GenBank and Malavi databases (accession IDs in parentheses). Bars to the right of tree represent the assignment of sequences to L. simondi clade A (teal), L. simondi clade B (orange), or other Leucocytozoon. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4. Phylogenetic tree depicting inferred genetic relationships among Haemoproteus mitochondrial DNA cytochrome b in Negligible evidence for detrimental effects of Leucocytozoon infections among Emperor Geese (Anser canagicus) breeding on the Yukon-Kuskokwim Delta, Alaska
Fig. 4. Phylogenetic tree depicting inferred genetic relationships among Haemoproteus mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the Yukon-Kuskokwim Delta, Alaska during 2006–2016 and those previously reported for closely related haemosporidian morphospecies on the National Center for Biotechnology Information GenBank and Malavi databases (accession IDs in parentheses).
Fig. 2. Minimum spanning network for haemosporidian mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the YukonKuskokwim Delta, Alaska during 2006–2016 in Negligible evidence for detrimental effects of Leucocytozoon infections among Emperor Geese (Anser canagicus) breeding on the Yukon-Kuskokwim Delta, Alaska
Fig. 2. Minimum spanning network for haemosporidian mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the YukonKuskokwim Delta, Alaska during 2006–2016. Circles are drawn proportional to the frequency at which haplotypes were detected. Shading represented the assignment of representative sequences for haplotypes to L. simondi clade A (teal), L. simondi clade B (orange), or other Leucocytozoon (grey) in phylogenetic analyses (see Results and Fig. 5). Lines are drawn proportional to genetic distance and are labeled per the number of mutations represented (except single nucleotide polymorphisms which are unlabeled). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
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