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... real. We estimated the maximum likelihood tree topology for 16s rRNA sequences (from the Ribosomal Database Project II, release 9, http://rdp.cme.msu.edu/, downloaded 3 May 2006) using PHYML Online (=-=Guindon et al., 2005-=-, http://atgc.lirmm.fr/phyml/, accessed 18 May 2006) with discrete gamma rate variation, four gamma categories, and a general time-reversible model. There is little correlation between the edge length...

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...mbination with a forward primer based on the sequence of the spliced leader described in (Zhang et al. 2007). New sequences were deposited in GenBank under accession numbers EU551745–EU551753. Phylogenetic Analyses Candidate O. marina genes with plastid ancestry were subject to phylogenetic analyses with a wide variety of homologues. Phylogenies were initially screened using a rapid Neighbor-Joining (NJ) analysis implemented in PAUP 4.0b10 (Swofford 2002). In cases where this did not exclude the possibility of a plastid origin, phylogenies were inferred by maximum likelihood (ML) using PhyML (Guindon et al. 2005) and Bayesian analysis usingMrBayes 3 (Ronquist and Huelsenbeck 2003). For ML, a WAG model of amino acid substitution was used with 8 categories of rate variation under a gamma distribution plus invariable sites. Bootstrap support was tested with 300 replicates under the same conditions. For Bayesian analyses, a gamma correction with 8 categories and proportion of invariable sites was used, and 4 Monte Carlo Markov chains were also used (default temperature 5 0.2). In each case, a total of 1,000,000 generations was calculated with trees sampled every 100 generations and with burn-in of 200,000...

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... proteins from other organisms were used to add structural information. The corresponding unrooted tree was constructed by a maximum likelihood method using PHYLM with the Jones-Taylor-Thornton model =-=(14)-=-. Drawing was realized using the Treeview program (30). Bootstrap values were computed by PHYLM for 100 replicates of the original data set. RESULTS YbdB protein is produced under iron limitation cond...

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...R DN1, and B5957 UP1 and LTR DN1, were used for the first and second rounds of PCR, respectively [48]. The SGA amplicons were sequenced from the start of V1 through the ectodomain of gp41 [Hxb2 numbering of positions 6600–8000]. Phylogenetic and compartmentalization analyses Nucleotide sequences of the env genes were aligned using Clustal W [49,50] or MAFFT software [51]. Sequences from each subject were codon aligned using GeneCutter (Los Alamos HIV-1 database; http://www.hiv.lanl.gov/content/sequence/GENE_ CUTTER/cutter.html). Maximum likelihood phylogenetic trees were generated using PhyML [52] with the following parameters: HKY85 nucleotide substitution model, four substitution rate categories, estimation of the transition/transversion rate ratio, estimation of the proportion of invariant sites, and estimation of the gamma distribution parameter [53]. Compartmentalization of CSF viral populations by sequence was determined using the Slatkin-Maddison test for compartmentalization [54] by HyPhy software [55] using 10,000 permutations. Pairwise distance was calculated for HIV-1 env sequences in the CSF-compartmentalized population using MEGA 4.1 software [56,57,58]. Construction of HI...

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...3) was assessed using the Goldman-Cox test (Goldman, 1993). For each Goldman-Cox test, we first estimated the ML topology for the dataset and model in question using PhyML (Guindon and Gascuel, 2003; =-=Guindon et al., 2005-=-). We then calculated both the unconstrained (i.e., model-free) and constrained (i.e., assuming a particular model) likelihoods for this topology, as well as the free parameters of the model, using PA...

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...tioned novel proteins. Sequence numbers correspond to those in figure 1 and can be found under the accession numbers: 1—AF086712; 2—L25662; 3—X99080; 4—AF018033; 5—M93690; 6—X51968; 7—D38414; 8—AF012049; 9—X06950; 10—M22874; 11—M14954; 12—M28878; 13—X60372; 14—U66331; 15—U88211; 16—AB005891; 17—U73800; 18— X60177; 19—U87543; 20—Z25525; 21—AF025462; 22—U58755; 23—M26915; 24—AF081114; 25—U93574; 26—X51967; 27—U13035; 28—M16558; 29—U29445; 30—M33009; 31—M62862; and 32—X17078. These sequences were then analyzed phylogenetically using the NJ andmaximum likelihood tree usingMEGA4.0 andPHYML online (Guindon et al. 2005), respectively. Results The GPS identified a total of 1,888 FL elements in the anole. Further Blast and BLAT searches of the anole genome using the sequences collected by GPS as probes failed to detect any other FL elements, although we recovered a number of truncated (TR) elements (supplementary fig. 1, Supplementary Material online). Representatives from five of the twelve clades of non-LTR retrotransposons were detected: L1, L2, CR1, RTE, and R4 (fig. 1). These clades differ greatly in copy number and diversity. Of the five clades that inhabit the genome of A. carolinensis, L1 is the least ...

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...than or equal to the score of the yeast Rex1 paralog. Sequences were aligned with MUSCLE (27). The phylogenetic tree was inferred from protein sequence alignments by maximum likelihood. We used Phyml =-=(28, 29)-=- under the Jones-Taylor-Thornton model of protein evolution (30) with site-tosite rate variation modeled on a discrete distribution (four categories, shape parameter , and proportion of invariable ...

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...tion for each node (Baker and 282 N.R. Lovejoy et al. / Molecular Phylogenetics and Evolution 54 (2010) 278–290DeSalle, 1997). Finally, we explored the effect of different character weighting schemes by inferring transition/transversion ratios from the data and using step matrices to differentially weight these state changes. We also subjected the dataset to phylogenetic analyses using maximum likelihood and Bayesian methods (Guindon and Gascuel, 2003; Ronquist and Huelsenbeck, 2003). Maximum likelihood phylogenetic methods were implemented in the program PHYML 3.0 (Guindon and Gascuel, 2003; Guindon et al., 2005), under the GTR+I+G model. This model was found to be the best fit for the unpartitioned molecular dataset, according to both hierarchical likelihood ratio tests (LRT) and Akaike Information Criterion (AIC), as implemented in Modeltest v3.7 (Posada and Crandall, 1998). For the likelihood analyses, bootstrapping methods (100 replicates) were used to assess the node support (Felsenstein, 1985b). Bayesian inference was performed in MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003). The morphological data and each of the three genes were treated as separate data partitions. All partitions had indepen...

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...hecked for invariant and conserved regions using GENEDOC (version 2.7; National Resource for Biomedical Supercomputing (Pittsburgh, PA) (14, 33). We used neighbor joining (NJ) as implemented in MEGA4 =-=(19, 20, 54)-=-. The bootstrap values for NJ trees were obtained after 1,000 generations, and MEGA4 tree viewer was used to visualize the trees and calculate confidence values (25, 54). 16S rRNA sequences were also ...

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...dard mammalian species tree was trimmed to only include the species in the alignment using prunetree (Ziheng Yang, unpublished). The gene trees were created from the nucleotide alignment using phyml (=-=Guindon et al., 2005-=-) with model TN93 (Tamura and Nei, 1993) and 4 rate categories in the discrete gamma models of rate variation among sites (Yang, 1994). 149Figure 6.4 Example of a species tree (A) and a gene tree (B)...