Locus | Basepair length | Genomic location | Phylo. sub. model | Diverg. sub. model |
---|
RHEB1 | 642 | Nuclear | T92 + G | TN93 + I |
TIMM17A | 516 | Nuclear | K2P | HKY |
TCF3 | 601 | Nuclear | T92 | HKY |
RPS24 | 407 | Nuclear | HKY | HKY |
SLC29A4 | 524 | Nuclear | TN93 + I | TN93 + I |
NFKBIZ | 506 | Nuclear | K2P | HKY |
G3PDH | 432 | Nuclear | HKY | HKY |
myoglobin | 677 | Nuclear | K2P | HKY |
ZENK | 653 | Nuclear | TN93 | TN93 |
ZENK 3’UTR | 287 | Nuclear | T92 | HKY |
COI | 699 | Mitochondrial | HKY + G | HKY + G |
cyt b | 1026 | Mitochondrial | HKY + G | HKY + G |
ADAMTS10 | 510 | Nuclear | K2 | -- |
HMGB2 | 575 | Nuclear | T92 + I | -- |
- Only the two mtDNA loci were treated as coding; the mtDNA were further partitioned by codon in the divergence time estimation analyses. Substitution models for each locus were estimated using MEGA 5.2 and the best available model was used in MEGA 5.2 and MrBayes 3.2.1 for the phylogenetic analyses and in BEAST 1.8.0 for the divergence time estimation analyses. ADAMTS10 and HMGB2 were only used in phylogenetic analysis testing flamingo intraspecific variation. Abbreviations: RHEB1, Rheb isoform 1, intron 3; TIMM17A, mitochondrial import inner membrane translocase subunit Tim17A, intron 3; TCF3, Transcription factor 3, intron 12; RPS24, ribosomal protein S24, intron 5; SLC29A4, solute carrier family 29, member 4, intron 8; NFKBIZ, Nuclear Factor of light polypeptide gene enhancer in B-cells inhibitor, zeta, intron 6; G3PDH, glyceraldehyde-3-phosphate dehydrogenase gene, intron 11; myoglobin gene, exon 2, 3 and intron 2; ZENK, zinc finger protein, exon 2; ZENK 3’UTR, zinc finger protein, 3’ untranslated region; COI, cytochrome oxidase subunit I; cyt b, cytochrome b; ADAMTS10, ADAM metallopeptidase with thrombospondin, type 1 motif, intron 5; HMGB2, high mobility protein group, box 2, intron 1. Drawings by M. McCracken.