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501 results for “Phylogenetic tree”
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
Data from: Tree phylogenetic diversity promotes host–parasitoid interactions
Evidence from grassland experiments suggests that a plant community's phylogenetic diversity (PD) is a strong predictor of ecosystem processes, even stronger than species richness per se. This has, however, never been extended to species-rich forests and host–parasitoid interactions. We used cavity-nesting Hymenoptera and their parasitoids collected in a subtropical forest as a model system to test whether hosts, parasitoids, and their interactions are influenced by tree PD and a comprehensive set of environmental variables, including tree species richness. Parasitism rate and parasitoid abundance were positively correlated with tree PD. All variables describing parasitoids decreased with elevation, and were, except parasitism rate, dependent on host abundance. Quantitative descriptors of host–parasitoid networks were independent of the environment. Our study indicates that host–parasitoid interactions in species-rich forests are related to the PD of the tree community, which influences parasitism rates through parasitoid abundance. We show that effects of tree community PD are much stronger than effects of tree species richness, can cascade to high trophic levels, and promote trophic interactions. As during habitat modification phylogenetic information is usually lost non-randomly, even species-rich habitats may not be able to continuously provide the ecosystem process parasitism if the evolutionarily most distinct plant lineages vanish.
Data from: Phylogenetics, delimitation and historical biogeography of the pantropical tree genus Thespesia (Malvaceae, Gossypieae)
Thespesia consists of 16 species of trees and shrubs from Southeast Asia–Oceania, Africa and America, the most well known being T. populnea, a small tree of tropical coastal areas around the world. Phylogenetic relationships in the genus and among its allies in tribe Gossypieae were inferred using three plastid and two nuclear regions to ascertain its generic delimitation and explore its biogeographical history. Maximum-likelihood and Bayesian analyses confirmed that Thespesia is not monophyletic and, based on these results, Azanza is reinstated to accommodate the two species previously placed in Thespesia section Lampas. Dating analyses and ancestral range estimation indicated that Thespesia s.s. most likely originated in Southeast Asia–Oceania c. 30 Mya, but extant species did not begin to differentiate until the late Miocene. Two dispersal events, one into Africa c. 11 Mya and another into America (Antilles) c. 9 Mya, gave rise to the African and the Greater Antillean endemics, respectively. The two most widespread hydrochorous species, T. populnea and T. populneoides, originated in Southeast Asia–Oceania from where they spread to other parts of the world. Our analysis also indicated a much earlier origin than previously reported for Eumalvoideae and its tribes, suggesting that vicariance might have had an important role early in the history of these groups.
Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification
Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using *BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for > 10 Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.
FIGURE 1. Bayesian phylogenetic tree inferred from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURE 1. Bayesian phylogenetic tree inferred from 621 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) gene sampled from the Rhamphus specimens originated from Italy. Bayesian a posteriori probabilities are shown above/below branches (values below 0.7 are omitted). Abbreviation: oxy = R. oxyacanthae; bav = R.bavierai n. sp.; ham = R. hampsicora n. sp.; mon = R. monzinii.
FIGURE 1 in The two-spotted spider mite Tetranychus urticae Koch and the carmine spider mite Tetranychus cinnabarinus (Boisduval) in China mixed in their Wolbachia phylogenetic tree
FIGURE 1. The phylogenetic tree of the wsp gene sequences of Wolbachia in 18 geographical populations of T. cinnabarinus, 13 geographical populations of T. urticae in China and T. urticae (red and green forms) from other countries. The wsp gene sequences of three insects (Drosophila simulans, Aedes albopictus and Culex pipiensis) were used as out groups.
FIGURE 2. Bayesian phylogenetic tree for 60 in Taxonomic reexamination of Portulaca okinawensis (Portulacaceae) in the Ryukyu Archipelago of Japan based on molecular and morphological data
FIGURE 2. Bayesian phylogenetic tree for 60 OTUs of Portulaca with three outgroups based on internal transcribed spacer (ITS) sequence. The topology of the maximum parsimony (MP) strict consensus tree was highly compatible with the Bayesian tree. Bayesian posterior probabilities (left) and bootstrap percentages in the MP analysis (right) are shown [see the Table 1 for the localities collection of the four ITS types (A–D) of P. okinawensis].
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 in Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 sequences inferred by the Neighbor-Joining method using the Kimura 2- parameter model; all bootstrap values over 50% are shown. Sequences obtained from the NCBI are marked with the sequence accession numbers. Aegilops tauschii sequence was defined as an outgroup in the analysis. Clades 1 and 2 are associated with Triticum monococcum s. lat. and T. urartu, respectively.
FIGURE 1. A in Reaching a compromise between conflicting nuclear and plastid phylogenetic trees: a new classification for the genus Cattleya (Epidendreae; Epidendroideae; Orchidaceae)
FIGURE 1. A comparison of the phylogenetic relationships between subgroups of Cattleya and related genera based on a Bayesian analyses of plastid and ITS sequence data (details of the data collection and analyses presented in van den Berg, 2009). Plastid regions: matK, trnL intron, trnL-F spacer, rps16, both introns of trnK, and atpB-rbcL and psbA-trnH spacers. Nuclear region: ITS.
FIGURE 3. Tree resulting from a in Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata)
FIGURE 3. Tree resulting from a twelve-partition maximum likelihood analysis of the combined 12S–16S and ND2–COI mtDNA genic sequence data. Species with two or more sampled individuals are numbered as in Table 1 for sample location. Filled circles on nodes represent maximum likelihood bootstrap values of ≥ 95. Numbers on branches are bootstrap values <95. Filled diamonds represent branches supported with parsimony bootstrap values ≥ 90, Bayesian posterior probabilities ≥ 0.95, and maximum likelihood bootstrap values ≥ 95.
FIGURE 2. Phylogenetic consensus tree among hermit crab species obtained from a in Molecular analysis validates of some informal morphological groups of Pagurus (Fabricius, 1775) (Anomura: Paguridae) from South America
FIGURE 2. Phylogenetic consensus tree among hermit crab species obtained from a fragment of Histone H3 (nDNA), inferred from Maximum Likelihood (ML) Maximum Parsimony (MP) and Neighbor-Joining (NJ) analysis. Topology of a ML is presented, with bootstrap values shown from left to right are for ML, MP and NJ respectively. Support numbers ≤ 50% are shown.
FIGURE 6. Strict consensus tree for 61 in Systematics and Phylogenetics of Indo-Pacific Luciolinae Fireflies (Coleoptera: Lampyridae) and the Description of new Genera
FIGURE 6. Strict consensus tree for 61 IP analysis; consensus of 163 MPT of length 2615 from phylogenetic analysis of 61 Indo-Pacific study group taxa. New genera, new species, and still undescribed species in red, bold. Bremer supports above branches.
Figure 2 in Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)
Figure 2. Phylogenetic tree showing the reconstructed ancestral geographical distributions for extant and ancestral drosophilids estimated by the maximum-likelihood algorithm. Extant geographical distributions were retrieved from the Drosophila Stock Center or from the ZipcodeZoo database. See Table S2 for geographical distributions.
Figure 1 in Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)
Figure 1. Timescale for drosophilids based on a maximum-likelihood (ML) analysis using a concatenated alignment (9917 bp) of six protein-coding nuclear genes. Several monophyletic branches have been collapsed, indicating that all taxa within that taxonomic rank form a cluster. Support values above branches are bootstrap proportions performed on the ML tree; values less than 50 are not shown.
FIGURE 2. Most parsimonious combined tree under equal weights, with 17 in Phylogenetic analysis of the Pantomorus-Naupactus complex (Coleoptera: Curculionidae: Entiminae) from North and Central America
FIGURE 2. Most parsimonious combined tree under equal weights, with 17 morphological characters coded as additive. Bootstrap values over 50% below the corresponding branches.
FIGURE 1. Most parsimonious morphological tree under equal weights, with 17 in Phylogenetic analysis of the Pantomorus-Naupactus complex (Coleoptera: Curculionidae: Entiminae) from North and Central America
FIGURE 1. Most parsimonious morphological tree under equal weights, with 17 morphological characters coded as additive. Bremer support values over 3 are given above each corresponding branch and bootstrap values over 50% are below the branches.
Figure 14. Pruned maximum credibility Bayesian trees. Dataset C in Redescription of the skull of the Australian flatback sea turtle, Natator depressus, provides new morphological evidence for phylogenetic relationships among sea turtles (Chelonioidea)
Figure 14. Pruned maximum credibility Bayesian trees. Dataset C based on the matrix from Evers & Benson (2019). Dataset D based on matrix from Evers & Benson (2019) with added characters found in this study. Colours at nodes represent base of clades. Numbers at the node show posterior probability value of node.
Figure 13. Maximum credibility Bayesian trees. Dataset A in Redescription of the skull of the Australian flatback sea turtle, Natator depressus, provides new morphological evidence for phylogenetic relationships among sea turtles (Chelonioidea)
Figure 13. Maximum credibility Bayesian trees. Dataset A based on the matrix from Evers & Benson (2019). Dataset B based on matrix from Evers & Benson (2019) with added characters found in this study. Different colours at nodes represent base of clades. Numbers at the node show posterior probability value of node.
Figure 3 in Amplified fragment length polymorphisms, the evolution of the land snail genus Theba (Stylommatophora: Helicidae), and an objective approach for relating fossils to internal nodes of a phylogenetic tree using geometric morphometrics
Figure 3. Thin plate splines illustrating shape changes between selected nodes of the tree in Figure 4 based on weighted branch lengths.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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