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12 results for “maximum likelihood method”
Рис. 1. Calyptra thalictri: 1 — Calyptra thalictri alexander ssp. n., гоΛотип; 2 — Calyptra thalictri alexander ssp. n., паратип; 3 — кΛаΑограмма Calyptra thalictri. Построена метоΑом максимаΛьного схоΑства, параметрическая моΑеΛь Тамура-Неи, 10 000 бутстрапрепΛикаций; 4 — биотоп Calyptra thalictri alexander ssp. n. Fig. 1. Calyptra thalictri: 1 — Calyptra thalictri alexander ssp. n., holotype; 2 — Calyptra thalictri alexander ssp. n., paratype; 3 — cladogram of Calyptra thalictri. Based on the maximum likelihood method, Tamura-Nei parametrical model, 10000 bootstrap replications; 4 — biotope of Calyptra thalictri alexander ssp. n. in A New Subspecies Of (Borkhausen, 1790) (Lepidoptera: Erebidae, Calpinae) From Kyrgyzstan
Рис. 1. Calyptra thalictri: 1 — Calyptra thalictri alexander ssp. n., гоΛотип; 2 — Calyptra thalictri alexander ssp. n., паратип; 3 — кΛаΑограмма Calyptra thalictri. Построена метоΑом максимаΛьного схоΑства, параметрическая моΑеΛь Тамура-Неи, 10 000 бутстрапрепΛикаций; 4 — биотоп Calyptra thalictri alexander ssp. n. Fig. 1. Calyptra thalictri: 1 — Calyptra thalictri alexander ssp. n., holotype; 2 — Calyptra thalictri alexander ssp. n., paratype; 3 — cladogram of Calyptra thalictri. Based on the maximum likelihood method, Tamura-Nei parametrical model, 10000 bootstrap replications; 4 — biotope of Calyptra thalictri alexander ssp. n.
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 2 in The maximum likelihood identification method applied to insect morphometric data
Figure 2. Classification based on landmarks (and semilandmarks). Values in percent are the proportions of correct assignments averaged over the complete set of data, mixing the various species, but restricted to the landmark-based method (including here the combination of landmarks and semilandmarks). Each value is shown with an error bar which is its standard deviation. The left part shows the results from the maximum likelihood method applied to the centroid size and to the shape variables. The right part shows the average scores obtained with the Mahalanobis classification. Abbreviation: first PC—the shape variables used were the few first PC of shape variables that the MLi classification selected as the most discriminant set of PC; all PC—the maximum number of PC that could be used by the Mahalanobis classification.
Figure 4 in The maximum likelihood identification method applied to insect morphometric data
Figure 4. Principal component analysis of sandfly data. The factor map of the two first principal components (PC) describing the morphospace of female sandfly data: S. bailyi, S. barraudi and P. stantoni. Unidentified males show a convex hull covering both female S. bailyi and S. barraudi, leaving two specimens outside the female hulls.
Figure 1 in The maximum likelihood identification method applied to insect morphometric data
Figure 1. Measurements on Triatominae. A. Digitization of the contour of the eggs of Triatomini and Rhodniini. B. Landmarks as digitized on the wing of Panstrongylus chinai. C. Traditional measurement of eggs of the tribe Triatomini (Panstrongylus sp. and Triatoma sp., left) and the tribe Rhodniini (Rhodnius sp., right). Abbreviation: op.dim—dimensions of the operculum; max.leng— maximum length; max.dim—maximum diameter.
Figure 3 in The maximum likelihood identification method applied to insect morphometric data
Figure 3. Classification based on harmonics. Values in percent are the proportions of correct assignments averaged over the complete set of data, mixing the various species, but restricted to the outline-based method. Each value is shown with an error bar which is its standard deviation. The left part shows the results from the maximum likelihood method applied to the perimeter of the contour and to the shape variables. The right part shows the average scores obtained with the Mahalanobis classification. Abbreviation: first PC— the shape variables used were the few first PC of shape variables that the MLi classification selected as the most discriminant set of PC; all PC—the maximum number of PC that could be used by the Mahalanobis classification.
FIGURE 7. Maximum Likelihood best tree for 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 7. Maximum Likelihood best tree for 33 specimens of Devadatta and one outgroup taxon from the combined COI+16S+ITS+28S data set. Bootstrap support values below 100 are superimposed on the tree. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
FIGURE 3. Phylogenetic tree inferred from maximum likelihood methods using 70 in Tigridiopalma longmenensis (Melastomataceae), a new species from Guangdong, China
FIGURE 3. Phylogenetic tree inferred from maximum likelihood methods using 70 protein-coding genes from the complete chloroplast genome sequences of Tigridiopalma longmenensis and other 15 species of Melastomataceae. The numbers beside the node indicate the bootstrap percentages (%) after 5000 replications of bootstrap sampling.
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S rRNA + COI sequence data, demonstrating the evolutionary relationships within the P. sidneyi s.l. species complex. Statistical support for nodes is provided as posterior probability values above nodes (> 0.95 PP) and bootstrap values below nodes (> 75%). An * or # denotes nodal relationships that were not supported (<0.95 PP/ <75%). Potamonautes sidneyi s.s. (clade 3) localities are marked with a dark blue triangle, while P. danielsi (clade 5) localities are marked by an orange square. The two new species, P. karooensis, (clade 2) and P. Ʋalles (clade 4), are marked by a light-blue circle and a green diamond, respectively. Specimens of P. barbarai are confined to clade 1.
Data from: Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics
Since their advent, supertrees have been increasingly used in large-scale evolutionary studies requiring a phylogenetic framework and substantial efforts have been devoted to developing a wide variety of supertree methods (SMs). Recent advances in supertree theory have allowed the implementation of maximum likelihood (ML) and Bayesian SMs, based on using an exponential distribution to model incongruence between input trees and the supertree. Such approaches are expected to have advantages over commonly used non-parametric SMs, e.g. matrix representation with parsimony (MRP). We investigated new implementations of ML and Bayesian SMs and compared these with some currently available alternative approaches. Comparisons include hypothetical examples previously used to investigate biases of SMs with respect to input tree shape and size, and empirical studies based either on trees harvested from the literature or on trees inferred from phylogenomic scale data. Our results provide no evidence of size or shape biases and demonstrate that the Bayesian method is a viable alternative to MRP and other non-parametric methods. Computation of input tree likelihoods allows the adoption of standard tests of tree topologies (e.g. the approximately unbiased test). The Bayesian approach is particularly useful in providing support values for supertree clades in the form of posterior probabilities.
Fig. 4. Bootstrap consensus tree inferred from 1000 replicates, using the Maximum Likelihood method. The analysis involved 20 in Severe coenurosis caused by larvae of Taenia serialis in an olive baboon (Papio anubis) in Benin
Fig. 4. Bootstrap consensus tree inferred from 1000 replicates, using the Maximum Likelihood method. The analysis involved 20 sequences of 12S rDNA gene of cestodes having coenurus type larvae (Taenia serialis and T. multiceps) and one sequence of Echinococcus granulosus, as outgroup. For each sequence, the GenBank Accession number, species, developmental stage, host and geographic origin are provided. A total of 320 positions were included in the dataset. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches.
Data from: Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics
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