Phylogenetic examination of pandemic H1 HA

Slides:

Advertisements

Similar presentations

Phylogenetic Tree A Phylogeny (Phylogenetic tree) or Evolutionary tree represents the evolutionary relationships among a set of organisms or groups of.

Advertisements

1 General Phylogenetics Points that will be covered in this presentation Tree TerminologyTree Terminology General Points About Phylogenetic TreesGeneral.

Summer Bioinformatics Workshop 2008 Comparative Genomics and Phylogenetics Chi-Cheng Lin, Ph.D., Professor Department of Computer Science Winona State.

Phylogenetic reconstruction

Multiple alignment June 29, 2007 Learning objectives- Review sequence alignment answer and answer questions you may have. Understand how the E value may.

Chapter 2 Opener How do we classify organisms?. Figure 2.1 Tracing the path of evolution to Homo sapiens from the universal ancestor of all life.

Molecular phylogenetics

Phylogenetics Alexei Drummond. CS Friday quiz: How many rooted binary trees having 20 labeled terminal nodes are there? (A) (B)

Phylogenetics and Coalescence Lab 9 October 24, 2012.

OUTLINE Phylogeny UPGMA Neighbor Joining Method Phylogeny Understanding life through time, over long periods of past time, the connections between all.

Phylogenetic Prediction Lecture II by Clarke S. Arnold March 19, 2002.

Introduction to Phylogenetic Trees

Chapter 8 Molecular Phylogenetics: Measuring Evolution.

Introduction to Phylogenetic trees Colin Dewey BMI/CS 576 Fall 2015.

Ayesha M.Khan Spring Phylogenetic Basics 2 One central field in biology is to infer the relation between species. Do they possess a common ancestor?

1 CAP5510 – Bioinformatics Phylogeny Tamer Kahveci CISE Department University of Florida.

Phylogeny and the Tree of Life

Pipelines for Computational Analysis (Bioinformatics)

Sequence and structure relatedness of matrix protein of human respiratory syncytial virus with matrix proteins of other negative-sense RNA viruses K.

Phylogenetic characterization of the Bunyavirales-like viruses identified in this study. Phylogenetic characterization of the Bunyavirales-like viruses.

Multiple Alignment and Phylogenetic Trees

Di Liu, Weifeng Shi, George F Gao

Endeavour to reconstruct the characters of each hypothetical ancestor.

Phylogenetic Trees.

A graphing calculator is required for some problems or parts of problems 2000.

Dots 5 × TABLES MULTIPLICATION.

Dots 5 × TABLES MULTIPLICATION.

Phylogeny and Modern Taxonomy

Dots 2 × TABLES MULTIPLICATION.

H3 HA amino acid mutations that were selected in indicated clades.

Dots 3 × TABLES MULTIPLICATION.

Dots 6 × TABLES MULTIPLICATION.

Volume 70, Issue 5, Pages (June 2011)

Dots 2 × TABLES MULTIPLICATION.

Centrality of targeted and neighboring proteins.

Maximum-likelihood phylogenetic tree of norovirus genomes belonging to genogroup GI, with the norovirus GII reference genome as an outlier. Maximum-likelihood.

Phylogenetic tree of perA A2-domain DNA sequence.

Phylogeny of Shiga toxin-encoding phage from SDi/SJo S. sonnei isolates. Phylogeny of Shiga toxin-encoding phage from SDi/SJo S. sonnei isolates. (A) progressiveMauve.

Congruence of the Peronosporales order among recent multilocus phylogenetic analyses. Congruence of the Peronosporales order among recent multilocus phylogenetic.

Dots 4 × TABLES MULTIPLICATION.

Sequence and structure relatedness of matrix protein of human respiratory syncytial virus with matrix proteins of other negative-sense RNA viruses K.

Maximum-likelihood phylogeny of the household isolates from core SNPs

Molecular data assisted morphological analyses

Fig. 3. H3N2 incidence forecasts based on the cluster model for the Unites States. H3N2 incidence forecasts based on the cluster model for the Unites States.

Maximum likelihood (ML) unrooted tree based on the full-length 16S rRNA genes (A) and 31 conserved single-copy genes (B) showing the phylogenetic position.

(A, left) Radial cladogram based on RAxML-based maximum-likelihood phylogeny (500 bootstraps, gamma distribution model, and LG+F substitution model) constructed.

(A) Tiled view of an ESOM map constructed using all 51 metagenome bins assembled from the samples collected in this study, with the white square encompassing.

Phylogeny of the novel rhabdoviruses identified by UHTS

Phylogenetic tree of 38 Pseudomonas type strains, based on the V3-V5 region sequence of the 16S rRNA gene (V3 primer, positions 442 to 492; and V5 primer,

Phylogenetic diversity of archaeal lineages in the great ape gut microbiome. Phylogenetic diversity of archaeal lineages in the great ape gut microbiome.

Successful spread and transmission of rifampin-resistant clones.

Phylogenetic Trees Jasmin sutkovic.

Modern Taxonomy traditional classification grouped species according to morphology (body, shape, size and other structural features) modern taxonomy is.

Maximum likelihood phylogeny of USA500 and other CC8 strains.

Phylogeny and the Tree of Life

Individuals (dots) colored according to results of hierarchical clustering of copy number estimates (as described in Supplementary Text) for IGHV

Visualization of lineage radius increase.

NP sequence alignment of human H1N1 strains and phylogenetic analysis of representative NP from pandemic and seasonal H1N1 strains. NP sequence alignment.

Phylogenetic analyses of alphacoronaviruses based on complete genome and ORF1ab protein sequence. Phylogenetic analyses of alphacoronaviruses based on.

Phylogenetic analysis of AquK2P.

Neighbor-joining tree of the 262 S

ITS rRNA gene locus. ITS rRNA gene locus. Schematic of the eukaryotic ribosomal gene cluster. The SILVA database contains sequences of the 18S gene, while.

Distribution of the diversity numbers of antibiotic resistance and virulence factor protein families by environmental metagenomes’ protein family richness.

Dots 3 × TABLES MULTIPLICATION.

S protein sequence-based phylogenetic analyses of alphacoronaviruses.

Synteny and Phylogeny of Putative GRMZM2G Orthologs.

Phylogenetic trees for fusion (F) and attachment (G) genes of selected HMPV isolates. Phylogenetic trees for fusion (F) and attachment (G) genes of selected.

Evolution-informed forecasting of seasonal influenza A (H3N2)‏

Phylogenetic analysis of complete Fusobacterium genomes.

Tree depicting the phylogenetic relationships of all strains included in this study. Tree depicting the phylogenetic relationships of all strains included.

Presentation transcript:

Phylogenetic examination of pandemic H1 HA Phylogenetic examination of pandemic H1 HA. Each phylogenetic branch and corresponding dot are colored according to their season (1 October to 30 March) and by calculated ΔΔG cluster (see Materials and Methods). Phylogenetic examination of pandemic H1 HA. Each phylogenetic branch and corresponding dot are colored according to their season (1 October to 30 March) and by calculated ΔΔG cluster (see Materials and Methods). (A) Maximum likelihood phylogeny of HA genes of 2,874 nonduplicate pdmH1N1 IAVs. (B to F) Graphs of estimated change in thermal stability of each HA as related to A/California/7/2009 HA over time. Each dot represents a unique HA sequence. Overlaid lines connect most likely ancestors (MLA) of each HA from the specified year back through time. Each line reflects the calculated lowest genetic difference (highest relatedness) between HA sequences from two seasons. Multiple lines were drawn for ties. Once the MLAs for the rightmost sequences were identified, these were the starting sequences for estimating the MLAs in the next prior season. This analysis was continued until the 2009 season for each starting season. In each season, fewer viruses were identified as being more closely related from the prior season, suggesting that there were genetic bottlenecks from one season to the next. Eili Y. Klein et al. mSphere 2018; doi:10.1128/mSphereDirect.00554-17