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Table 1 Summary of significant changes in relative rate found in a sample of 46 concatenated alignments of vertebrate-specific CNEs, grouped according to their location in the proximate genomic region of key developmental genes

From: Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals

Group

Sub-clade

Species

CNE alignment defined by genomic region:

All species

  

NR2F2 (H), SALL3 (H)

 

Carnivora

 

FIGN (H), SHOX (L)

  

A. melanoleuca

IRX1/2/4 (H)

  

C. familiaris

IRX3/5/6 (L)

 

Cetartiodactyla

 

BHLHB5 (H), DACH1 (H), FOXP1 (H), IRX1/2/4 (H), MAF (H), SOX3 (H), TFAP2A (H)

  

B. taurus

NR2F1(H), POU3F3 (H), ZIC2 (H)

  

T. truncatus

BARHL2 (H), BCL11A (H), FIGN (H), HMX2/3 (H), LHX1 (H), MEIS1 (H), MEIS2 (H), PAX2 (H), SHOX (L), SOX6 (H), SOX21 (H), TSHZ1(H)

 

Chiroptera

 

SHH (H), TSHZ1 (H)

 

Yinpterochiroptera

 

IRX1/2/4 (H)

 

Echolocating Yinpterochiroptera

 

FOXP1 (H), HMX2/3 (H), SOX3 (H), SOX6 (H)

  

M. lyra

BARHL2 (H), BCL11A (H), BHLHB5 (H), DACH1 (H), EMX2 (H), ESRRB (H), FIGN (H), IRX3/5/6 (H), MAF (H), MEIS1(H), MEIS2 (H), NR2F1 (H), TFAP2A (H), ZFHX1B (H), ZIC1 (H)

  

R. ferrumequinum

NA

 

Old World fruit bats

 

FIGN (H), IRX3/5/6 (H)

  

E. helvum

NR2F1 (H)

  

P. vampyrus

BCL11A (H), DLX1 (H), GLI3 (H), SOX3 (H), SOX6 (H)

 

Yangochiroptera

 

BARHL2 (H), BHLHB5 (H), EMX2 (H), FIGN (H), FOXP1 (H), HMX2/3 (H), IRX3/5/6 (H), MEIS2 (H), SOX6 (H)

  

P. parnellii

DACH1 (H), NR2F1 (H), POU3F3 (H), SOX2 (H), SOX3 (H), SOX21 (H), ZIC2 (H)

  

M. lucifugus

BCL11A (H), DLX1 (H), ZFHX1B (H), ZIC1 (H)

  1. Significant differences in relative rates are defined as P-values less than 0.05 following Holm’s correction method for the multiple comparisons made. Higher rate in focal taxon – (H); lower rate in focal taxon – (L).