Table 2.
Phylogenetic evidence of HGT in neighbouring genes
| Species | IMG Locus_tag a | IMG product name | Tree label b | # taxa | # sites | Adjacent taxa in tree |
|---|---|---|---|---|---|---|
| Methanomassiliicoccus luminyensis B10 | missing (Mlum65) | NADP oxidoreductase, coenzyme F420-dependent | T01 | 85 | 146 | Alpha-, Deltaproteobacteria |
| Ca. Kuenenia stuttgartiensis | kustc0379 | Unknown protein | T02 | 47 | 368 | div. BRC1 bacterium; Gammaproteobacteria |
| " | kustc0382 | Glutamate formimidoyltransferase | T03 | 85 | 484 | Marine euryarchaeotes |
| " | kustc0383 | Glutaredoxin-like protein | T04 | 39 | 74 | Firmicutes |
| " | kustc0384 | Permease of the major facilitator superfamily | T05 | 61 | 389 | Deltaproteobacteria |
| Planctomycetaceae bacterium KSU-1 | missing (KSU_979) | Indole-3-glycerol phosphate synthase | T06 | 74 | 238 | Acidobacteria |
| " | missing (KSU_981) | Conserved hypothetical protein | T07 | 63 | 88 | Deltaproteobacteria |
| Ca. Brocadia anammoxidans WQC04 | missing (Brocad1) | Indole-3-glycerol phosphate synthase | see T06 | |||
| " | missing (Brocad3) | Predicted membrane protein | see T07 | |||
| Nitrosomonas europaea ATCC 19718 | NE0446 | 3-demethylubiquinone-9-3-methyltransferase | T08 | 76 | 156 | Gammaproteobacteria |
| " | NE0447 | 3-methyladenine DNA glycosylase I | T09 | 59 | 189 | Gammaproteobacteria |
| " | NE0449 | Aspartate and glutamate racemase | T10 | 45 | 238 | Gammaproteobacteria |
| Nitrosomonas sp. AL212 | NAL212_0966 | Hypothetical protein | T11 | 51 | 141 | Gammaproteobacteria |
| Geobacter sp. M21 | GM21_1429 | Diguanylate cyclase | T12 | 55 | 156 | Gammaproteobacteria |
Phylogenetic Bayesian inference was carried out in PhyloBayes, ML inference in RAxML and PhyML. Number of taxa and sites in the alignment are given. All BI analyses were run to convergence (maxdiff < 0.1 and eff. size >100). ML in RAxML used “-f a” option with 1,000 rapid-bootstrap replicates. ML in PHyML used SPR tree-space search strategy with 5 random starts + BioNJ. Prottest best-fitting model was LG + Г4 + F for T05, T07, T09, T10, datasets, LG + Г4 for all the others. See Additional file 1: Table S4 for full data
aWhen Integrated Microbial Genomes (IMG) locus tag was missing, an arbitrary one was chosen
bAll trees in Additional file 3