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Table 1 Biodiversity estimates for each method and marker

From: Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

gene\methods BCG lower limit
(nj tree)
BCG higher limit
(nj tree)
MYC
(UPGMA tree)
206 sequences of CO1 without EM 129 ESUs
i = 0,0087
37 ESUs
i = 0,137
121 ESUs
(117-129)
206 sequences of CO1
with EM (HKY85)
130 ESUs
i = 0,01
38 ESUs
i = 0,259
128 ESUs
(118-130)
206 sequences of CO1
with EM (GTR+I+G)
55 ESUs
i = 0,620
64 ESUs
i = 0,531
128 ESUs
(125-129)
206 sequences of psbA
without EM
52 ESUs
i = 0,066
52 ESUs
i = 0,071
90 ESUs
(74-101)
206 sequences of psbA
with EM (HKY85)
54 ESUs
i = 0,075
11 ESUs
i = 0,224
91 ESUs
(61-94)
206 sequences of psbA
with EM (GTR+I+G)
55 ESUs
i = 0,081
63 ESUs
i = 0,047
81 ESUs
(35-100)
  1. Each column corresponds to the results of a given method. Each line was inferred with specific settings and evolutionary models (EM). Uncorrected p-distances were calculated using MEGA 4.1[112]. Parameters for two evolutionary models (HKY85; GTR with a gamma distribution splitting into 4 categories - GTR+I+G4) were calculated using PALM http://palm.iis.sinica.edu.tw/index.html and MrModeltest version 2.2[113], and then used to calculate corrected p-distances using PAUP* version 4b10[114]. NJ (Neighbor-Joining) and UPGMA trees were built using PAUP* version 4b10, considering no evolution model and then a HKY85, and finally a GTR+I+G model. A 'relative time from branching rate' was determined with the UPGMA trees using the GENIE v3.0 software[115]. Since it was not possible to identify a barcode gap unambigously, we defined a range of BCG estimates, based on the histogram of p-distances. The first empty class of frequency defined the lower limit for the intraspecific distance (BCG lower limit). The higher limit of the intraspecific distance (BCG higher limit) was defined as the left bound of the 95% confidence interval of the Normal distribution followed by the histograms of p-distances. The number of estimated monophyletic groups corresponding to species (ESUs) is indicated in bold. Values of i correspond to the upper bound estimated for the intraspecific pairwise-distance for the BCG methods. For the MYC method, a range of estimated ESUs is given into rounded bracket (confidence interval of 95%).