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33 results for “multi-locus phylogeny”
FIGURE 3 in Multi-locus phylogeny supports the placement of Endocarpon pulvinatum within Staurothele s. str. (lichenised ascomycetes, Eurotiomycetes, Verrucariaceae)
FIGURE 3. Most likely unrooted tree (with BS values) showing the relationships within the genus Staurothele based on ITS. The collection number in bold (BMC 12394) represents E. tortuosum (= E. pulvinatum). The scale bar represents the number of nucleotide substitutions/site.
FIGURE 3 in Multi-locus phylogeny reveals Phaeodothis mori sp. nov. (Didymosphaeriaceae, Pleosporales) from dead leaves of Morus australis
FIGURE 3. Phaeodothis tricuspidis (SF125876, holotype) a. Herbarium packet and specimen. b. Ascomata on host. c. Close up of ascoma. d, e. Sections through ascomata. f. Peridium comprising hyaline compressed cells. g–j. Mature and immature asci surrounded by pseudoparaphyses. k–n. ascospores. Scale bars: c = 1000 µm, d, e = 100 µm, f = 20 µm, g–j = 30 µm, k–n = 5 µm.
FIGURE 2 in Multi-locus phylogeny reveals Phaeodothis mori sp. nov. (Didymosphaeriaceae, Pleosporales) from dead leaves of Morus australis
FIGURE 2. Phaeodothis mori (holotype, MFLU 18-2612) a, b. Appearance of ascomata on the host. c. Section of ascoma. d. Section of peridium. e. Pseudoparaphyses. f–i. Asci. j–l. Ascospores. m. Ascospores stained in Indian ink showing mucilaginous sheath. n. Germinated ascospore. o. Colony from below. p. Colony from above. Scale bars: c = 50 µm, d = 10 µm, e–i = 20 µm, j–n = 5 µm.
FIGURE 1 in Multi-locus phylogeny reveals Phaeodothis mori sp. nov. (Didymosphaeriaceae, Pleosporales) from dead leaves of Morus australis
FIGURE 1. RAxML tree based on a combined dataset of ITS, LSU, SSU and tef1- α partial sequences of 84 taxa of the family Didymosphaeriaceae. Bootstrap support values for maximum likelihood (ML), maximum parsimony (MP) values higher than 60% and Bayesian posterior probabilities (BYPP) greater than 0.90 are given above each branch respectively. The new isolates are in red. Ex-type strains are in bold. The tree is rooted by Pleospora herbarum (CBS 191.86, IT 956) and P. tarda (CBS 714.68).
FIGURE 3 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 3. The three different types of palea apices. A1—biapiculate (sinus shallow) palea apex of Yushania niitakayamensis (Hayata) P.-C. Keng (1957: 357) and A2—biapiculate (sinus shallow) palea apex of Bergbambos tessellata; B1—long-divided tips (sinus deep) palea of Arundinaria gigantea and B2—long-divided tips (sinus deep) palea of Fargesia spathacea Franchet (1893: 1067); C1—acute, undivided palea apex of A. debilis and C2—acute, undivided palea apex of Oldeania alpina (K. Schum.) Stapleton (2013: 100).
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16–trnQ, trnC– rpoB, trnD–trnT, trnT–trnL and ndhF 3' the PIC values include the outgroups. For the regions psbD-trnT, psbJ-petA and ycf6- psbM the PIC values include only the ingroup species.
FIGURE 2 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 2. Strict consensus of 1019 most parsimonious trees based on the five-region cpDNA dataset (rps16–trnQ, trnC–rpoB, trnD–trnT, trnT–trnL, ndhF 3'). Shaded region indicates the well supported Sri Lankan Arundinaria clade. Numbers indicate bootstrap values ≥ 70% from MP and ML analyses and posterior probabilities ≥ 0.95 from the BI analyses, respectively. Note that Clade XI is not shown in the tree because it was unsampled.
DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies
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Data from: Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)
Non-homogeneous processes and, in particular, base compositional non-stationarity have long been recognized as a critical source of systematic error. But only a small fraction of current molecular systematic studies methodically examine and effectively account for the potentially confounding effect of non-stationarity. The problem is especially overlooked in multi-locus or phylogenomic scale analyses, in part because no efficient tools exist to accommodate base composition heterogeneity in large data sets. We present a detailed analysis of a data set with 20 genes and 214 taxa to study the phylogeny of flatfishes (Pleuronectiformes) and their position among percomorphs. Most genes vary significantly in base composition among taxa and fail to resolve flatfish monophyly and other emblematic groups, suggesting that non-stationarity may be causing systematic error. We show a strong association between base compositional bias and topological discordance among individual gene partitions and their inferred trees. Phylogenetic methods applying non-homogeneous models to accommodate non-stationarity have relatively minor effect to reduce gene tree discordance, suggesting that available computer programs applying these methods do not scale up efficiently to the data set of modest size analysed in this study. By comparing phylogenetic trees obtained with species tree (STAR) and concatenation approaches, we show that gene tree discordance in our data set is most likely due to base compositional biases than to incomplete lineage sorting. Multi-locus analyses suggest that the combined phylogenetic signal from all loci in a concatenated data set overcomes systematic biases induced by non-stationarity at each partition. Finally, relationships among flatfishes and their relatives are discussed in the light of these results. We find support for the monophyly of flatfishes and confirm findings from previous molecular phylogenetic studies suggesting their close affinity with several carangimorph groups (i.e., jack and allies, barracuda, archerfish, billfish and swordfish, threadfin, moonfish, beach salmon, and snook and barramundi).
Data from: Multi-locus phylogeny of lethal amanitas: implications for species diversity and historical biogeography
Background: Lethal amanitas (Amanita section Phalloideae) are a group of wild, fatal mushrooms causing many poisoning cases worldwide. However, the diversity and evolutionary history of these lethal mushrooms remain poorly known due to the limited sampling and insufficient gene fragments employed for phylogenetic analyses. In this study, five gene loci (nrLSU, ITS, rpb2, ef1-α and β-tubulin) with a widely geographic sampling from East and South Asia, Europe, North and Central America, South Africa and Australia were analysed with maximum-likelihood, maximum-parsimony and Bayesian inference methods. Biochemical analyses were also conducted with intention to detect amatoxins and phalloidin in 14 representative samples. Result: Lethal amanitas were robustly supported to be a monophyletic group after excluding five species that were provisionally defined as lethal amanitas based on morphological studies. In lethal amanitas, 28 phylogenetic species were recognised by integrating molecular phylogenetic analyses with morphological studies, and 14 of them represented putatively new species. The biochemical analyses indicated a single origin of cyclic peptide toxins (amatoxins and phalloidin) within Amanita and suggested that this kind of toxins seemed to be a synapomorphy of lethal amanitas. Molecular dating through BEAST and biogeographic analyses with LAGRANGE and RASP indicated that lethal amanitas most likely originated in the Palaeotropics with the present crown group dated around 64.92 Mya in the early Paleocene, and the East Asia–eastern North America or Eurasia–North America–Central America disjunct distribution patterns were primarily established during the middle Oligocene to Miocene. Conclusion: The cryptic diversity found in this study indicates that the species diversity of lethal amanitas is strongly underestimated under the current taxonomy. The intercontinental sister species or sister groups relationships among East Asia and eastern North America or Eurasia–North America–Central America within lethal amanitas are best explained by the diversification model of Palaeotropical origin, dispersal via the Bering Land Bridge, followed by regional vicariance speciation resulting from climate change during the middle Oligocene to the present. These findings indicate the importance of both dispersal and vicariance in shaping the intercontinental distributions of these ectomycorrhizal fungi.
Data from: Multi-locus phylogeny of the Afrotropical freshwater crab fauna reveals historical drainage connectivity and transoceanic dispersal since the Eocene
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Data from: Multi-locus phylogeny of lethal amanitas: implications for species diversity and historical biogeography
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Data from: Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)
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