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E for PhyML, and so the closest alternative was chosen where
Bayesian posterior probability (PP) values were calculated using MRBAYES 3.1.2 [33] and are shown for the major clades on the ML phylogenies. Markov Chain Monte Carlo (MCMC) searches were performed, with four chains of 10,000,000 generations and trees sampled every 100. The first 10,000 trees sampled were discarded as `burn-in,‘ as Firms, nations, and also other aggregates. These agents exchange facts, rules, behaviors determined using Tracer v 1.4 [34], and a consensus topology and posterior probability values were calculated with the remaining trees. Pically an intuitive method. Perceivers then consider a variety of details components en Unrooted statistical parsimony networks were built using TCS 1.21 [35] at the 95 confidence limit. Population differentiation was assessed using Arlequin population pairwise fixation index (FST) values, with significance (P < 0.05) based on 1023 random permutations of the data. Populations with only one sample were excluded from these analyses. Arlequin was also used to perform AMOVA analyses on these data sets to assess the relative influence of withinand among-population variance. Historic population expansions were assessed in the broadly distributed COI clades (clades 1 and 4 for both taxa) by Fu‘s neutrality test [36] and mismatch distribution analysis [37], using Arlequin version 3.5 [38]. No other clades were examined as only broad-scale (trans-oceanic) expansions were relevant to the hypotheses and, as the mitochondrial marker was the most informative for each taxon, expansion tests were only carried out on COI data. Most Adenocystis samples shared a single LSU sequence (sequence 1A in Figure S2). Adenocystis utricularis COI clades were monophyletic with respect to all outgroups. For the A. utricularis rbcL phylogeny, the position of Utriculidium durvillaei could not be resolved. Bostrychia intricata was monophyletic with respect to outgroups for COI, consistent with the well-supported branches of the rbcL and LSU phylogenies (Figures S3 and S4). Given the high level of genetic divergence observed among clades within each of the study taxa (up to 9 for A. utricularisPermitsCollection permits for these non-endangered, non-protected seaweed species were not required for sampling in New Zealand and Chile. Collection permits from the sub-Antarctic islands were required, as these vulnerable environmental areas are protected by various administering authorities. For Macquarie Island, a permit for collection of samples was issued by the Department of Primary Industries, Parks, Water and Environment (Tasmania) (permit number 10001), with approval from the Macquarie Island Advisory Group. For Marion Island, a permit for collection was issued by the South African Department of Environmental Affairs (permit reference RES2010/11). For Gough Island, a permit for collection was issued by Tristan da Cunha Conservation. For the Falkland Islands, a collection permit was issued by the Falkland Islands Government (Research license R21/ 2009), and for South Georgia, by the Government of South Georgia (issue date 18 December 2009). The population pairwise FST analyses (Supplementary tables S6 and S7) indicate that some disjunct populations were genetically similar (note that, as sample sizes at several populations were low, these results should be interpreted cautiously). For example, for B. intricata, Falkland Island and several Chilean populations were not significantly differentiated. Nevertheless, in some po.E for PhyML, and so the closest alternative was chosen where appropriate). Node support was estimated by bootstrapping [32], with heuristic analysis of 1000 replicate data sets.
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