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Table 1 Congruence between mtDNA, nucDNA, and combined-data trees

From: What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodonsalamanders and 13 other vertebrate clades

Clade Total nodes Concordant nodes Discordant nodes Strongly supported discordance Weak mtDNA, strong nucDNA Strong mtDNA, weak nucDNA Weakly supported discordance Strong discordance resolved favoring mtDNA
Balistid fish 23 39% 61% 14% 43% 21% 21% 50%
mtDNA,
P = 0.5000
Scarine fish 40 55% 45% 44% 22% 17% 17% 75% mtDNA,
P = 0.1094
Hemiphractid frogs 40 45% 55% 36% 18% 23% 23% 75% mtDNA,
P = 0.1094
Hylid frogs 76 54% 46% 17% 29% 9% 46% 67% mtDNA,
P = 0.2344
Plethodon salamanders 51 33% 67% 56% 21% 24% 0% 79% mtDNA,
P = 0.0074
Phrynosomatid lizards 35 49% 51% 28% 44% 17% 11% 0% mtDNA,
P = 0.0313
Alcid birds 21 67% 33% 29% 14% 43% 14% 100% mtDNA, P = 0.2500
Caprimulgid birds 55 56% 44% 17% 4% 33% 46% 50% mtDNA,
P = 0.3750
Cotingid birds 35 63% 37% 23% 31% 0% 46% 67% mtDNA, P = 0.3750
Dicaeid birds 28 36% 64% 17% 11% 39% 33% 33% mtDNA,
P = 0.3750
Emydid turtles 36 33% 67% 29% 33% 17% 21% 38% mtDNA,
P = 0.2734
Cervid mammals 23 30% 70% 19% 0% 56% 25% 67% mtDNA, P = 0.3750
Murid rodents
(Philippines)
55 58% 42% 9% 43% 13% 35% 50% mtDNA,
P = 0.5000
Murid rodents (Sahul) 60 70% 30% 39% 22% 17% 22% 0% mtDNA, P = 0.0078
  1. Each column reports the percentage of total nodes (second column) that fall into the following categories: (a) concordant nodes are those present in the combined-data tree that are also present in both mtDNA and nucDNA trees; (b) discordant nodes are absent in one or both of the trees from the separate data sets; (c) strongly supported discordance indicates branches for which conflicting resolutions in mtDNA and nucDNA are strongly supported (Pp ≥ 0.95) by each one; (d) weak mtDNA (or nucDNA), strong nucDNA (or mtDNA) indicates branches for which conflicting resolutions were weakly supported by one (mtDNA or nucDNA) and strongly supported by the other; (e) weakly supported discordance indicates branches for which conflicting resolutions in mtDNA and nucDNA are weakly supported by both; (f) the far-right column gives the proportion of nodes with strongly supported discordance that are resolved in favor of the mtDNA in the combined-data tree. P-values indicate whether the number of these resolutions favoring mtDNA data are significantly different from random (exact binomial, p = 0.50). Significant P-values are bold faced.