Additional file 5 of New insights into the molecular phylogeny, biogeographical history, and diversification of Amblyomma ticks (Acari: Ixodidae) based on mitogenomes and nuclear sequences
Creators: name: Uribe, Juan E.
name: Kelava, Samuel
name: Nava, Santiago
name: Cotes-Perdomo, Andrea P.
name: Castro, Lyda R.
name: Rivera-Paéz, Fredy A.
name: Perea, Silvia
name: Mans, Ben J.
name: Gofton, Alexander
name: Teo, Ernest J. M.
name: Zardoya, Rafael
name: Barker, Stephen C.
Publisher: name: figshare
Year: 2024
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences

description: Additional file 5: Figure S1. a Phylogenetic tree based on mt genome data: Topology 1 with 15 concatenated genes at nucleotide codification (protein-coding and ribosomal genes). Bayesian tree was reconstructed using the best fit evolutionary model and partition scheme. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. b Phylogenetic tree based on mt genome data: Topology 2 with 15 concatenated genes at nucleotide codification (protein-coding and ribosomal genes) implemented GBlock to trim the alignment. Bayesian tree was reconstructed using the best fit evolutionary model and partition scheme. Numbers at nodes are statistical support values for posterior probability. The scale bar is in expected substitutions/site. c Phylogenetic tree based on mt genome data: Topology 3 with 15 concatenated genes at nucleotide codification (protein-coding and ribosomal genes). Maximum-Likelihood tree was reconstructed using the best fit evolutionary model and partition scheme. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. d Phylogenetic tree based on mt genome data: Topology 4 with 15 concatenated genes at nucleotide codification (protein-coding and ribosomal genes) implemented GBlock to trim the alignment. Maximum-likelihood tree was reconstructed using the best fit evolutionary model and partition scheme. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. e Phylogenetic tree based on mt genome data: Topology 5 with 15 concatenated genes at nucleotide codification (protein-coding and ribosomal genes). Maximum-likelihood tree was reconstructed using the best fit evolutionary model for the concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. f Phylogenetic tree based on mt genome data: Topology 6 with 15 concatenated genes at nucleotide codification (protein-coding and ribosomal genes) implemented GBlock to trim the alignment. Maximum-likelihood tree was reconstructed using the best fit evolutionary model for the concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. g Phylogenetic tree based on mt genome data: Topology 7 with 13 concatenated genes at amino acid codification (protein-coding genes). Maximum-likelihood tree was reconstructed using the best fit evolutionary model for the concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. h Phylogenetic tree based on mt genome data: Topology 8 with 13 concatenated genes at amino acid codification (protein-coding genes) implemented GBlock to trim the alignment. Maximum-likelihood tree was reconstructed using the best fit evolutionary model for the concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. i Phylogenetic tree based on mt genome data: Topology 9 with 13 concatenated genes at amino acid codification (protein-coding genes). Bayesian tree was reconstructed using CAT-GTR evolutionary model for concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. j Phylogenetic tree based on mt genome data: Topology 10 with 13 concatenated genes at amino acid codification (protein-coding genes) implemented GBlock to trim the alignment. Bayesian tree was reconstructed using CAT-GTR evolutionary model for concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. k Phylogenetic tree based on mt genome data: Topology 11 with 13 concatenated genes at amino acid codification (protein-coding genes). Maximum-likelihood tree was reconstructed using mixture evolutionary model for concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site. l Phylogenetic tree based on mt genome data: Topology 12 with 13 concatenated genes at amino acid codification (protein-coding genes) implemented GBlock to trim the alignment. Maximum-likelihood tree was reconstructed using mixture evolutionary model for concatenated matrix. Numbers at nodes are statistical support values for bootstrap proportions. The scale bar is in expected substitutions/site.