MBE Advance Access originally published online on October 12, 2005
Molecular Biology and Evolution 2006 23(2):254-267; doi:10.1093/molbev/msj030
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Article |
Application of Phylogenetic Networks in Evolutionary Studies
* Center for Bioinformatics (ZBIT), Tübingen University, Tübingen, Germany; and Department of Mathematics, Auckland University, Auckland, New Zealand
E-mail: huson{at}informatik.uni-tuebingen.de.
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.
Key Words: phylogeny • networks • software • confidence intervals
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. Roos and T. Heikkila Evaluating methods for computer-assisted stemmatology using artificial benchmark data sets Lit Linguist Computing, December 1, 2009; 24(4): 417 - 433. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Decker, J. C. Pires, G. C. Conant, S. D. McKay, M. P. Heaton, K. Chen, A. Cooper, J. Vilkki, C. M. Seabury, A. R. Caetano, et al. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics PNAS, November 3, 2009; 106(44): 18644 - 18649. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. R. Khan, J.-Y. Hu, S. Riss, C. He, and H. saedler MPF2-Like-A MADS-Box Genes Control the Inflated Calyx Syndrome in Withania (Solanaceae): Roles of Darwinian Selection Mol. Biol. Evol., November 1, 2009; 26(11): 2463 - 2473. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Boto Horizontal gene transfer in evolution: facts and challenges Proc R Soc B, October 28, 2009; (2009) rspb.2009.1679v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. D. Pirie, A. M. Humphreys, N. P. Barker, and H. P. Linder Reticulation, Data Combination, and Inferring Evolutionary History: An Example from Danthonioideae (Poaceae) Syst Biol, October 21, 2009; (2009) syp068v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Ogura, T. Ooka, A. Iguchi, H. Toh, M. Asadulghani, K. Oshima, T. Kodama, H. Abe, K. Nakayama, K. Kurokawa, et al. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli PNAS, October 20, 2009; 106(42): 17939 - 17944. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. T. Walk, E. W. Alm, D. M. Gordon, J. L. Ram, G. A. Toranzos, J. M. Tiedje, and T. S. Whittam Cryptic Lineages of the Genus Escherichia Appl. Envir. Microbiol., October 15, 2009; 75(20): 6534 - 6544. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Miklos, A. Novak, R. Satija, R. Lyngso, and J. Hein Stochastic models of sequence evolution including insertion--deletion events Statistical Methods in Medical Research, October 1, 2009; 18(5): 453 - 485. [Abstract] [PDF]
|
|
|
|
 |
|
 G. Lozano, H. P. Trenado, R. A. Valverde, and J. Navas-Castillo Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications J. Gen. Virol., October 1, 2009; 90(10): 2550 - 2562. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Schwarz, P. N. Seibel, S. Rahmann, C. Schoen, M. Huenerberg, C. Muller-Reible, T. Dandekar, R. Karchin, J. Schultz, and T. Muller Detecting species-site dependencies in large multiple sequence alignments Nucleic Acids Res., October 1, 2009; 37(18): 5959 - 5968. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Kadlec, R. Ehricht, S. Monecke, U. Steinacker, H. Kaspar, J. Mankertz, and S. Schwarz Diversity of antimicrobial resistance pheno- and genotypes of methicillin-resistant Staphylococcus aureus ST398 from diseased swine J. Antimicrob. Chemother., September 25, 2009; (2009) dkp350v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Zhaxybayeva, W. F. Doolittle, R. T. Papke, and J. P. Gogarten Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus Gen Biol Evol, September 23, 2009; 2009(0): 325 - 339. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Leache Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus) Syst Biol, September 21, 2009; (2009) syp057v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Q. Minh, S. Klaere, and A. von Haeseler Taxon Selection under Split Diversity Syst Biol, September 21, 2009; (2009) syp058v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Caro-Quintero, G. P. Rodriguez-Castano, and K. T. Konstantinidis Genomic Insights into the Convergence and Pathogenicity Factors of Campylobacter jejuni and Campylobacter coli Species J. Bacteriol., September 15, 2009; 191(18): 5824 - 5831. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. C. Springman, D. W. Lacher, G. Wu, N. Milton, T. S. Whittam, H. D. Davies, and S. D. Manning Selection, Recombination, and Virulence Gene Diversity among Group B Streptococcal Genotypes J. Bacteriol., September 1, 2009; 191(17): 5419 - 5427. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kaser, J. Hauser, P. Small, and G. Pluschke Large Sequence Polymorphisms Unveil the Phylogenetic Relationship of Environmental and Pathogenic Mycobacteria Related to Mycobacterium ulcerans Appl. Envir. Microbiol., September 1, 2009; 75(17): 5667 - 5675. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. C. Springman, J. L. Jacobs, V. S. Somvanshi, G. W. Sundin, M. H. Mulks, T. S. Whittam, P. Viswanathan, R. L. Gray, J. J. LiPuma, and T. A. Ciche Genetic Diversity and Multihost Pathogenicity of Clinical and Environmental Strains of Burkholderia cenocepacia Appl. Envir. Microbiol., August 15, 2009; 75(16): 5250 - 5260. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Dagan and W. Martin Getting a better picture of microbial evolution en route to a network of genomes Phil Trans R Soc B, August 12, 2009; 364(1527): 2187 - 2196. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Leache, M. S. Koo, C. L. Spencer, T. J. Papenfuss, R. N. Fisher, and J. A. McGuire From the Cover: Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma) PNAS, July 28, 2009; 106(30): 12418 - 12423. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. E. Roberts, E. J. Sargis, and L. E. Olson Networks, Trees, and Treeshrews: Assessing Support and Identifying Conflict with Multiple Loci and a Problematic Root Syst Biol, June 16, 2009; (2009) syp025v3. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. H. Huson, R. Rupp, V. Berry, P. Gambette, and C. Paul Computing galled networks from real data Bioinformatics, June 15, 2009; 25(12): i85 - i93. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Misof and K. Misof A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments: A More Objective Means of Data Exclusion Syst Biol, May 20, 2009; (2009) syp006v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Thomas, O. Dauwalder, V. Brun, C. Badiou, T. Ferry, J. Etienne, F. Vandenesch, and G. Lina Staphylococcus aureus Superantigens Elicit Redundant and Extensive Human V{beta} Patterns Infect. Immun., May 1, 2009; 77(5): 2043 - 2050. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Lackner, N. Mobius, K. Scherlach, L. P. Partida-Martinez, R. Winkler, I. Schmitt, and C. Hertweck Global Distribution and Evolution of a Toxinogenic Burkholderia-Rhizopus Symbiosis Appl. Envir. Microbiol., May 1, 2009; 75(9): 2982 - 2986. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Fu, O. Bannach, H. Chen, J.-H. Teune, A. Schmitz, G. Steger, L. Xiong, and W. B. Barbazuk Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA Genome Res., May 1, 2009; 19(5): 913 - 921. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. E. Wallace, S. G. Weller, W. L. Wagner, A. K. Sakai, and M. Nepokroeff Phylogeographic patterns and demographic history of Schiedea globosa (Caryophyllaceae) on the Hawaiian Islands Am. J. Botany, May 1, 2009; 96(5): 958 - 967. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Lott, A. Spillner, K. T. Huber, and V. Moulton PADRE: a package for analyzing and displaying reticulate evolution Bioinformatics, May 1, 2009; 25(9): 1199 - 1200. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. D. Manning, A. C. Springman, E. Lehotzky, M. A. Lewis, T. S. Whittam, and H. D. Davies Multilocus Sequence Types Associated with Neonatal Group B Streptococcal Sepsis and Meningitis in Canada J. Clin. Microbiol., April 1, 2009; 47(4): 1143 - 1148. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Moynihan, J. P. Morrissey, E. R. Coppoolse, W. J. Stiekema, F. O'Gara, and E. F. Boyd Evolutionary History of the phl Gene Cluster in the Plant-Associated Bacterium Pseudomonas fluorescens Appl. Envir. Microbiol., April 1, 2009; 75(7): 2122 - 2131. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Cuthbertson, I. L. Mainprize, J. H. Naismith, and C. Whitfield Pivotal Roles of the Outer Membrane Polysaccharide Export and Polysaccharide Copolymerase Protein Families in Export of Extracellular Polysaccharides in Gram-Negative Bacteria Microbiol. Mol. Biol. Rev., March 1, 2009; 73(1): 155 - 177. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Bilhere, P. M. Lucas, O. Claisse, and A. Lonvaud-Funel Multilocus Sequence Typing of Oenococcus oeni: Detection of Two Subpopulations Shaped by Intergenic Recombination Appl. Envir. Microbiol., March 1, 2009; 75(5): 1291 - 1300. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. D. Marshall, M. W. Coulson, and S. M. Carr Near Neutrality, Rate Heterogeneity, and Linkage Govern Mitochondrial Genome Evolution in Atlantic Cod (Gadus morhua) and Other Gadine Fish Mol. Biol. Evol., March 1, 2009; 26(3): 579 - 589. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. P. French, A. Midwinter, B. Holland, J. Collins-Emerson, R. Pattison, F. Colles, and P. Carter Molecular Epidemiology of Campylobacter jejuni Isolates from Wild-Bird Fecal Material in Children's Playgrounds Appl. Envir. Microbiol., February 1, 2009; 75(3): 779 - 783. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Deletoile, D. Decre, S. Courant, V. Passet, J. Audo, P. Grimont, G. Arlet, and S. Brisse Phylogeny and Identification of Pantoea Species and Typing of Pantoea agglomerans Strains by Multilocus Gene Sequencing J. Clin. Microbiol., February 1, 2009; 47(2): 300 - 310. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. C. Pratt, G. C. Gibb, M. Morgan-Richards, M. J. Phillips, M. D. Hendy, and D. Penny Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors Mol. Biol. Evol., February 1, 2009; 26(2): 313 - 326. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Deloger, M. El Karoui, and M.-A. Petit A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera J. Bacteriol., January 1, 2009; 191(1): 91 - 99. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. van Berkum and J. J. Fuhrmann Evidence from Internally Transcribed Spacer Sequence Analysis of Soybean Strains that Extant Bradyrhizobium spp. Are Likely the Products of Reticulate Evolutionary Events Appl. Envir. Microbiol., January 1, 2009; 75(1): 78 - 82. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. K. Rudd, R. M. Endicott, C. Friedman, M. Walker, J. M. Young, K. Osoegawa, NISC Comparative Sequencing Program, P. J. de Jong, E. D. Green, and B. J. Trask Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event Genome Res., January 1, 2009; 19(1): 33 - 41. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Lysak, M. A. Koch, J. M. Beaulieu, A. Meister, and I. J. Leitch The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae Mol. Biol. Evol., January 1, 2009; 26(1): 85 - 98. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-Q. He, Z.-X. Xie, G.-Z. Han, J.-B. Dong, D. Wang, J.-B. Liu, L.-Y. Ma, X.-F. Tang, X.-P. Liu, Y.-S. Pang, et al. Homologous Recombination as an Evolutionary Force in the Avian Influenza A Virus Mol. Biol. Evol., January 1, 2009; 26(1): 177 - 187. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. R. Bordenstein, C. Paraskevopoulos, J. C. Dunning Hotopp, P. Sapountzis, N. Lo, C. Bandi, H. Tettelin, J. H. Werren, and K. Bourtzis Parasitism and Mutualism in Wolbachia: What the Phylogenomic Trees Can and Cannot Say Mol. Biol. Evol., January 1, 2009; 26(1): 231 - 241. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Galtier and V. Daubin Dealing with incongruence in phylogenomic analyses Phil Trans R Soc B, December 27, 2008; 363(1512): 4023 - 4029. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. Claesson, D. van Sinderen, and P. W. O'Toole Lactobacillus phylogenomics - towards a reclassification of the genus Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2945 - 2954. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. F. Windram, P. Shaw, P. Robinson, and C. J. Howe Dante's Monarchia as a test case for the use of phylogenetic methods in stemmatic analysis Lit Linguist Computing, December 1, 2008; 23(4): 443 - 463. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Whitfield, S. A. Cameron, D. H. Huson, and M. A. Steel Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees Syst Biol, December 1, 2008; 57(6): 939 - 947. [Full Text] [PDF]
|
|
|
|
|
|
M. Arenas, G. Valiente, and D. Posada Characterization of Reticulate Networks Based on the Coalescent with Recombination Mol. Biol. Evol., December 1, 2008; 25(12): 2517 - 2520. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. W. Innes, C. Ameline-Torregrosa, T. Ashfield, E. Cannon, S. B. Cannon, B. Chacko, N. W.G. Chen, A. Couloux, A. Dalwani, R. Denny, et al. Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean Plant Physiology, December 1, 2008; 148(4): 1740 - 1759. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Isabel, E. Leblanc, M. Boissinot, D. K. Boudreau, M. Grondin, F. J. Picard, E. A. Martel, N. J. Parham, P. S. G. Chain, D. E. Bader, et al. Divergence among Genes Encoding the Elongation Factor Tu of Yersinia Species J. Bacteriol., November 15, 2008; 190(22): 7548 - 7558. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. S. Druzhinina, M. Komon-Zelazowska, L. Kredics, L. Hatvani, Z. Antal, T. Belayneh, and C. P. Kubicek Alternative reproductive strategies of Hypocrea orientalis and genetically close but clonal Trichoderma longibrachiatum, both capable of causing invasive mycoses of humans Microbiology, November 1, 2008; 154(11): 3447 - 3459. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. J. Derieg, A. Sangaumphai, and L. P. Bruederle Genetic diversity and endemism in North American Carex section Ceratocystis (Cyperaceae) Am. J. Botany, October 1, 2008; 95(10): 1287 - 1296. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Kim, Y. Kook, Y.-J. Yun, C. G. Park, N. Y. Lee, T. S. Shim, B.-J. Kim, and Y.-H. Kook Proportions of Mycobacterium massiliense and Mycobacterium bolletii Strains among Korean Mycobacterium chelonae-Mycobacterium abscessus Group Isolates J. Clin. Microbiol., October 1, 2008; 46(10): 3384 - 3390. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. M. W. Nye Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies Syst Biol, October 1, 2008; 57(5): 785 - 794. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. S. Renner, G. W. Grimm, G. M. Schneeweiss, T. F. Stuessy, and R. E. Ricklefs Rooting and Dating Maples (Acer) with an Uncorrelated-Rates Molecular Clock: Implications for North American/Asian Disjunctions Syst Biol, October 1, 2008; 57(5): 795 - 808. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. T. Holder, J. Sukumaran, and P. O. Lewis A Justification for Reporting the Majority-Rule Consensus Tree in Bayesian Phylogenetics Syst Biol, October 1, 2008; 57(5): 814 - 821. [Full Text] [PDF]
|
|
|
|
 |
|
 M. Mentel, V. Zimorski, P. Haferkamp, W. Martin, and K. Henze Protein Import into Hydrogenosomes of Trichomonas vaginalis Involves both N-Terminal and Internal Targeting Signals: a Case Study of Thioredoxin Reductases Eukaryot. Cell, October 1, 2008; 7(10): 1750 - 1757. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Jones, F. J. Leigh, I. Mackay, M. A. Bower, L. M.J. Smith, M. P. Charles, G. Jones, M. K. Jones, T. A. Brown, and W. Powell Population-Based Resequencing Reveals That the Flowering Time Adaptation of Cultivated Barley Originated East of the Fertile Crescent Mol. Biol. Evol., October 1, 2008; 25(10): 2211 - 2219. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Li, J. Wang, S. J. Rossiter, G. Jones, J. A. Cotton, and S. Zhang The hearing gene Prestin reunites echolocating bats PNAS, September 16, 2008; 105(37): 13959 - 13964. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. L. Sole, A. D. S. Bastos, and C. H. Scholtz Intraspecific Patterns of Mitochondrial Variation in Natural Population Fragments of a Localized Desert Dung Beetle Species, Pachysoma gariepinum (Coleoptera: Scarabaeidae) J. Hered., September 1, 2008; 99(5): 464 - 475. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Mereda Jr., I. Hodalova, P. Martonfi, J. Kucera, and J. Lihova Intraspecific Variation in Viola suavis in Europe: Parallel Evolution of White-flowered Morphotypes Ann. Bot., September 1, 2008; 102(3): 443 - 462. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Vieira, E. Teles, R. A. M. Santos, and C. P. Vieira Recombination at Prunus S-Locus Region SLFL1 Gene Genetics, September 1, 2008; 180(1): 483 - 491. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. H. Kloepper, C. N. Kienle, and D. Fasshauer SNAREing the Basis of Multicellularity: Consequences of Protein Family Expansion during Evolution Mol. Biol. Evol., September 1, 2008; 25(9): 2055 - 2068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Jacobson, G. Lin, T. S. Whittam, and E. A. Johnson Phylogenetic analysis of Clostridium botulinum type A by multi-locus sequence typing Microbiology, August 1, 2008; 154(8): 2408 - 2415. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Dagan, Y. Artzy-Randrup, and W. Martin Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution PNAS, July 22, 2008; 105(29): 10039 - 10044. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. M. Codoner and S. F. Elena The promiscuous evolutionary history of the family Bromoviridae J. Gen. Virol., July 1, 2008; 89(7): 1739 - 1747. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Tooming-Klunderud, B. Mikalsen, T. Kristensen, and K. S. Jakobsen The mosaic structure of the mcyABC operon in Microcystis Microbiology, July 1, 2008; 154(7): 1886 - 1899. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Watanabe, T. Ohi-Toma, and J. Murata Multiple hybridization in the Aristolochia kaempferi group (Aristolochiaceae): evidence from reproductive isolation and molecular phylogeny Am. J. Botany, July 1, 2008; 95(7): 885 - 896. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. Afset, E. Anderssen, G. Bruant, J. Harel, L. Wieler, and K. Bergh Phylogenetic Backgrounds and Virulence Profiles of Atypical Enteropathogenic Escherichia coli Strains from a Case-Control Study Using Multilocus Sequence Typing and DNA Microarray Analysis J. Clin. Microbiol., July 1, 2008; 46(7): 2280 - 2290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Gruenheit, P. J. Lockhart, M. Steel, and W. Martin Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites Mol. Biol. Evol., July 1, 2008; 25(7): 1512 - 1520. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. P. P. Almeida, F. E. Nascimento, J. Chau, S. S. Prado, C.-W. Tsai, S. A. Lopes, and J. R. S. Lopes Genetic Structure and Biology of Xylella fastidiosa Strains Causing Disease in Citrus and Coffee in Brazil Appl. Envir. Microbiol., June 15, 2008; 74(12): 3690 - 3701. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. R. Holland, A. C. Clarke, and H. M. Meudt Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution Syst Biol, June 1, 2008; 57(3): 347 - 366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Yan, H. Liu, T. J. Mohr, J. Jenrette, R. Chiodini, M. Zaccardelli, J. C. Setubal, and B. A. Vinatzer Role of Recombination in the Evolution of the Model Plant Pathogen Pseudomonas syringae pv. tomato DC3000, a Very Atypical Tomato Strain Appl. Envir. Microbiol., May 15, 2008; 74(10): 3171 - 3181. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S.-q. Zuo, P.-h. Zhang, J.-f. Jiang, L. Zhan, X.-m. Wu, W.-j. Zhao, R.-m. Wang, F. Tang, Z. Dun, and W.-c. Cao Seoul Virus in Patients and Rodents from Beijing, China Am J Trop Med Hyg, May 1, 2008; 78(5): 833 - 837. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Weiss-Schneeweiss, K. Tremetsberger, G. M. Schneeweiss, J. S. Parker, and T. F. Stuessy Karyotype Diversification and Evolution in Diploid and Polyploid South American Hypochaeris (Asteraceae) Inferred from rDNA Localization and Genetic Fingerprint Data Ann. Bot., May 1, 2008; 101(7): 909 - 918. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Gonzalez-Escalona, J. Martinez-Urtaza, J. Romero, R. T. Espejo, L.-A. Jaykus, and A. DePaola Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing J. Bacteriol., April 15, 2008; 190(8): 2831 - 2840. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. J. De Lange, P. B. Heenan, D. J. Keeling, B. G. Murray, R. Smissen, and W. R. Sykes Biosystematics and Conservation: A Case Study with Two Enigmatic and Uncommon Species of Crassula from New Zealand Ann. Bot., April 1, 2008; 101(6): 881 - 899. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Birin, Z. Gal-Or, I. Elias, and T. Tuller Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion Bioinformatics, March 15, 2008; 24(6): 826 - 832. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Jonczyk, H. Schmidt, A. Osterrieder, A. Fiesselmann, K. Schullehner, M. Haslbeck, D. Sicker, D. Hofmann, N. Yalpani, C. Simmons, et al. Elucidation of the Final Reactions of DIMBOA-Glucoside Biosynthesis in Maize: Characterization of Bx6 and Bx7 Plant Physiology, March 1, 2008; 146(3): 1053 - 1063. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-L. Y. Ong, G. C. Ulett, A. N. Mabbett, S. A. Beatson, R. I. Webb, W. Monaghan, G. R. Nimmo, D. F. Looke, A. G. McEwan, and M. A. Schembri Identification of Type 3 Fimbriae in Uropathogenic Escherichia coli Reveals a Role in Biofilm Formation J. Bacteriol., February 1, 2008; 190(3): 1054 - 1063. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. W. Leigh, E. Susko, M. Baumgartner, and A. J. Roger Testing Congruence in Phylogenomic Analysis Syst Biol, February 1, 2008; 57(1): 104 - 115. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. W. Grimm and T. Denk ITS Evolution in Platanus (Platanaceae): Homoeologues, Pseudogenes and Ancient Hybridization Ann. Bot., February 1, 2008; 101(3): 403 - 419. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Penny, W. T. White, M. D. Hendy, and M. J. Phillips A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals Mol. Biol. Evol., February 1, 2008; 25(2): 239 - 242. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. van Berkum, Y. Badri, P. Elia, M. E. Aouani, and B. D. Eardly Chromosomal and Symbiotic Relationships of Rhizobia Nodulating Medicago truncatula and M. laciniata Appl. Envir. Microbiol., December 1, 2007; 73(23): 7597 - 7604. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Jing, R. Johnson, A. Seres, G. Kiss, M. J. Ambrose, M. R. Knox, T. H. N. Ellis, and A. J. Flavell Gene-Based Sequence Diversity Analysis of Field Pea (Pisum) Genetics, December 1, 2007; 177(4): 2263 - 2275. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Kilian, H. Ozkan, A. Walther, J. Kohl, T. Dagan, F. Salamini, and W. Martin Molecular Diversity at 18 Loci in 321 Wild and 92 Domesticate Lines Reveal No Reduction of Nucleotide Diversity during Triticum monococcum (Einkorn) Domestication: Implications for the Origin of Agriculture Mol. Biol. Evol., December 1, 2007; 24(12): 2657 - 2668. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. C. Miller, M. Andrews-Cookson, and C. H. Daugherty Two Patterns of Variation among MHC Class I Loci in Tuatara (Sphenodon punctatus) J. Hered., November 21, 2007; (2007) esm095v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. B. Rounge, T. Rohrlack, A. Tooming-Klunderud, T. Kristensen, and K. S. Jakobsen Comparison of Cyanopeptolin Genes in Planktothrix, Microcystis, and Anabaena Strains: Evidence for Independent Evolution within Each Genus Appl. Envir. Microbiol., November 15, 2007; 73(22): 7322 - 7330. [Abstract] [Full Text] [PDF]
|
|