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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.