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226 results for “phylogenetic reconstruction”
FIGURE 2 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 2. Syntopic species of Tropidurus found at the Reserva Particular do Patrimônio Natural Fazenda Pé da Serra, Serra do Arame, Ibotirama, Bahia, Brazil, and their respective habitats: (A, B) T. sertanejo, n. sp. (MZUSP 104274, allotype); (C, D) T. hispidus (MZUSP 104276); (E, F) T. pinima (MZUSP 104271).
FIGURE 6 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 6. Allotype of Tropidurus sertanejo, n. sp. (MZUSP 104274): (A) head in dorsal view; (B) head in ventral view; (C) head in lateral view; (D) dorsal body illustrating the spotted pattern typical of the new species; (E) ventral body showing the unpigmented underside of the thighs and cloacal flap characteristic of females.
FIGURE 5 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 5. Holotype of Tropidurus sertanejo, n. sp. (MZUSP 104273): (A) head in dorsal view; (B) head in ventral view showing intense pigmentation toward gular region; (C) head in lateral view; (D) dorsal body; (E) ventral body showing the typical dark flash marks on the underside of the thighs and cloacal flap of adult males.
FIGURE 15 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 15. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus on four mitochondrial (12S, 16S, CO1, Cyt b) and six nuclear loci (BACH1, kif24, NTF3, PRLR, PTPN, SNCAIP). Numbers associated to nodes refer to bootstrap values.
FIGURE 1. Taxonomic curve showing a in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 1. Taxonomic curve showing a steep, nonasymptotic increment in the number of species of the lizard genus Tropidurus described since 1820. Specimen of T. sertanejo, n. sp., MZUSP 104274 (allotype).
FIGURE 14 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 14. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus based on four nuclear (BACH1, kif24, NTF3, PRLR, PTPN, SNCAIP) loci. Numbers associated to nodes refer to bootstrap values.
FIGURE 13 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 13. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus based on four mitochondrial (12S, 16S, CO1, Cyt b) loci. Numbers associated to nodes refer to bootstrap values.
FIGURE 11 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 11. Boxplot showing variation in scale counts among Tropidurus species (ordinated by mean): (Tcat) T. catalanensis, (Tchr) T. chromatops, (Tcoc) T. cocorobensis, (Tery) T. erythrocephalus, (Teth) T. etheridgei, (This) T. hispidus, (Thyg) T. hygomi, (Timb) T. imbituba, (Tins) T. insulanus, (Tita) T. itambere, (Tmon) T. montanus, (Tmuc) T. mucujensis, (Tore) T. oreadicus, (Tpsa) T. psammonastes, (Tser) T. sertanejo, n. sp. (highlighted in dark gray.), (Ttor) T. torquatus.
FIGURE 4 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 4. Measurements used for morphometric analyses of Tropidurus. Abbreviations: AL, arm length; EOS, ear opening–snout distance; FAL, forearm length; FOL, foot length; HDL, hand length; HH, head height; HW, head width; SL, shank length; SVL, snout-vent length; THL, thigh length; TL, tail length.
FIGURE 3 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 3. Map on left shows the distribution of the Brazilian biomes and highlights the State of Bahia, predominantly covered by the semiarid Caatinga. Map on right (altimetric profile) shows the distribution of Tropidurus sertanejo, n. sp.: northernmost dot indicates the type locality (RPPN Fazenda Pé da Serra, Serra do Arame, Ibotirama, Bahia: 12° 08′ 45.21 S, 43° 03′ 20.83 W) and southernmost dot indicates the only known additional locality of occurrence of the new species (Caetité, Bahia: 14° 04′ 17.82 S, 42° 29′ 48.33″ W).
FIGURE 12 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 12. Scatterplot of LD1 and LD2 generated by the discriminant analysis performed on the scale counts of Tropidurus. See table 8 for corresponding summary statistics. Tropidurus sertanejo, n. sp., highlighted in dark gray.
FIGURE 10 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 10. Scatterplot of PC1 and PC2 generated by the principal component analyses and LD1 and LD2 generated by the size-free discriminant analyses performed on the log-transformed morphometric variables of Tropidurus. Tropidurus sertanejo, n. sp., highlighted in dark gray. See table 5 for corresponding summary statistics.
Figure 4 in An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature
Figure 4. Right scapulocoracoid and humerus of Cygnus buccinator showing osteological features and muscle origins (shaded) and insertions (unshaded). Scapulocoracoid in lateral view (posterior aspect of coracoid) (A) and medial view (anterior aspect of coracoid) (B). Arrows in B indicate extent of the M. rhomboideus superficialis insertion onto the anterior edge of the scapular blade. Right coracoid in lateral (C) and medial (D) views. Humerus in ventral (E) and dorsal (F) views. Not drawn to scale. Lower-case abbreviations are skeletal elements and ligaments, upper-case abbreviations are muscles.
Figure 1 in An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature
Figure 1. Diagrammatic representation of the theropod right scapulocoracoid. A, developmental orientation and terminology. B, positional orientation of a non-eumaniraptoran theropod scapulocoracoid. C, positional orientation of an eumaniraptoran scapulocoracoid. Abbreviations: A, anterior; D, dorsal; L, lateral; M, medial; P, posterior; V, ventral.
Figure 12 in An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature
Figure 12. Reconstructed right shoulder girdle and upper arm musculature of Saurornitholestes langstoni in anterior aspect. Shaded muscles are those not illustrated in Figure 11A. The reconstructed furcula is based on that of Velociraptor (Appendix). Ulna/radius is diagrammatic. Arrows superimposed onto reconstructed muscles indicate mean direction of muscle action. See text for further details, and for muscle abbreviations. Superscripts: 1, unequivocal muscle with scar; 2, unequivocal muscle with no scar.
Figure 3 in An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature
Figure 3. Right scapulocoracoid and humerus of Caiman sp. showing osteological features and muscle origins (shaded) and insertions (unshaded). Scapulocoracoid in lateral (A) and medial (B) views, and humerus in ventral (C), dorsal (D) and anterior (E) views. Not drawn to scale. In B, the origin of M. costocoracoideus profundus is from the medial scapulosternal ligament. Lower-case abbreviations are skeletal elements and ligaments, upper-case abbreviations are muscles.
Figure 10 in An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature
Figure 10. Flow chart of the cascade of inferences used to determine the presence of shoulder girdle muscles in theropods, their topology of attachment and their functional attributes. This stepwise methodology is similar to that of Bryant & Russell (1992).
Figure 6 in An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature
Figure 6. Right shoulder girdle elements of Saurornitholestes langstoni (TMP 88.121.39) showing osteological features and proposed muscle origins (shaded) and insertions (not shaded). Coracoid in lateral (A) and medial (B) views. The posterior coracoid process was reconstructed based on that of Velociraptor mongoliensis (Appendix). Scapula in lateral (C) and medial (D) views. Arrows in D indicate extent of RS insertion onto the anterior edge of the scapular blade. The acromion process was reconstructed based on that of Velociraptor mongoliensis (Appendix). Humerus in ventral (E) and dorsal (F) views. See text for muscle abbreviations (in upper-case letters). Skeletal elements are not to scale.
Figure 5 in An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature
Figure 5. Right scapulocoracoid and humerus of Struthio camelus showing osteological features and muscle origins (shaded) and insertions (unshaded). Scapulocoracoid in lateral (A) and medial (B) views, and humerus in ventral (C) and dorsal (D) views. Not drawn to scale. Dorsomedial curvature of the scapulocoracoid is removed. In A, the insertion of the M. pectoralis is onto the Ligamentum sternocoracoideum laterale. Lower-case abbreviations are skeletal elements, upper-case abbreviations are muscles.
Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments
<p><span>Machine learning can be as good as maximum likelihood when reconstructing phylogenetic topologies and determining the best evolutionary model on four taxon alignments.</span></p> <p><span>Phylogenetic tree reconstruction with molecular data is important in many fields of life science research. The gold standard in this discipline is the Maximum Likelihood tree reconstruction method. Here we show that for quartet trees, Machine Learning using neural networks can be as good as the Maximum Likelihood method to infer the best tree topology and the best model of sequence evolution for nucleotide as well as amino acid sequences. For this purpose we simulated data sets for a wide range of branch lengths, evolutionary models and model parameters and compared the topologies and inferred models obtained with Machine learning with those obtained with the Maximum Likelihood and the Neighbour Joining method. Our results show that neural networks are a promising avenue for determining relatedness between taxa, which is likely to accelerate the construction of phylogenetic trees in the future, while maintaining a high accuracy.</span></p>
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