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Table 2 Genetic loci used in the phylogenetic and divergence time estimation analyses

From: A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae)

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 --
  1. 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.