Table 1 Candidate genes for positive/relaxed selection inferred by CODEML (branch model – bm, branch-site model - bsm), aBSREL, and RELAX (K > 1) which we could assign to biological functions suggested as related to cold adaptation in previous studies (see References within the table) on the basis of their GeneCards description.

From: Selection-driven adaptation to the extreme Antarctic environment in the Emperor penguin

Function/metabolism of

CODEML (bm)

CODEML (bsm)

aBSREL

Relax (K > 1)

Relax (K < 1)

GO ID

Previously identified genes

References

Cardiovascular activity and regulation

  

DNASE1, ADAMTS13, EIF2AK1, MYBPC3, UBA5, ENTPD1, NRP1, PKDCC, ROCK2, LMOD2, PLEKHM2, ATP11C, HGSNAT, TFRC, UFL1, SPIC, MYOCD, STXBP4, FBLN5, MYLK3, AGXT2, FLVCR1

AGXT2, MYLK3

FLVCR1, EDRF1

GO:0072359 (adj p-val = 0.01); GO:0060047 (adj p-val = 0.04); GO:0003306 (adj p-val = 0.02)*; GO:1901863 (adj p-val = 0.03)*

SPTBN5, KNG1, ICAM4, DSP, TNN, ARID5B, CUL7, EHD3, VCL, ALPK3, XIRP1, ADORA2B, SOD1, POMC, CD36, ENPEP, MME, BDKRB2

Yudin et al. 2017; Liu et al. 2014; Wollenberg Valero et al. 2014; Vianna et al. 2020

Skin thickness

  

PRDM5, KIAA1211, EGF, FAM83G, MATN3, DSC1, SGSM3, GAB1, RAB11FIP1, ASAH1

ASAH1

  

DSP, EXPH5, EVPL, DSG1

Yudin et al. 2017; Li et al.2014

Feathers development

WNT3A, RPL31**

WNT3A

SHOC2, RPL31**, WNT3A

RPL31**

  

(beta-keratin gene families)

Li et al. 2014

Immunity

DHX36, ANKRD17, TEC, SLIT2, TRIM29

DHX36, ANKRD17

MILR1, TRAF3IP2, SH2D4B, SPPL2B, MAP3K5, TBK1, IFIH1, RASGRP1, IFIT5, PLD4, CD101, LGALS8, ASB9, CMAS, AOAH, C7, MRC1, JCHAIN, HERC5, ATG5, LTA4H, ANKRD17, TRIM29

HERC5, ATG5, LTA4H, DHX36, TEC

ANKRD17

GO:0002376 (adj p-val = 0.0002); GO:0006952 (adj p-val = 0.01); GO:0032607 (adj p-val = 0.02)

SELPLG, ZDBF2, MAPK1, MAPK14

Yudin et al. 2017

Lipid and fatty acid

ASAP1

 

FAAH, VTG2, LEPR, PLCXD1, OSBPL2, LMAN1, PPARA, FADS1, ACSBG2, FNDC3B, GK5, ARSK, PDZRN3, DECR2, ACOT7, ACOX3, KIAA1468, PCCA, ACOT12, VPS13A

HMGCL, PCCA, ACOT12, VPS13A

ASAP1

GO:0006631 (adj p-val = 0.04); GO:0006071 (adj p-val = 0.05); GO:0033993 (adj p-val = 0.03)*

NR1D2, LPL, CETP, SOD1, LEPR, APOB, ABCC6, UCP3, FASN, GLPTD1, AKT2, SLC38A4, SFI1

Kumar et al. 2015; Yudin et al. 2017; Castruita et al. 2020; Liu et al. 2014; Tigano et al. 2018; Wollenberg Valero et al. 2014; Li et al. 2014; Lin et al. 2019

Glucose (including insulin)

ADCY5, IDE, SLC2A1, PAK1

IDE, PAK1

AAED1, ALG6, SLC17A9, ABCA10, TTYH3, ABCC8, GRB14, GAB1, PHKB, STXBP4, NRG4, SLC7A6, AGL, PGM2L1, IDE, ADCY5, SLC2A1

SLC7A6, AGL, PGM2L1, SFI1

PAK1

GO:0071333 (adj p-val = 0.05)*

SFI1, SLC38A4, AKT2, GLPTD1

Kumar et al. 2015; Yudin et al. 2017

Thyroid hormones

  

NCOA3, MARCH6

  

GO:0009725 (adj p-val = 0.03)

THRB, RARB

Tigano et al. 2018

Non-shivering thermogenesis

  

PRDM16, L2HGDH, CACNA1D, ATP1A1

   

UCPs, avUCP, THRB, RARB, NR1D2

Lowell and Spiegelman 2000; Talbot et al. 2004; Tigano et al.2018

Shivering thermogenesis

      

NEB, ADORA2B, SOD1, HSPB2

Yudin et al. 2017; Wollenberg Valero et al. 2014

Response to oxidative stress

GMEB1, ATOX1

GMEB1

MAP3K5, PTGR2, SELENOP, COQ6, GMEB1, PEX16

COQ6

VRK2

 

SOD1, UCP3

Wollenberg Valero et al. 2014

Stress response

  

EIF2AK1, CUL4B, MAP3K3, ULK2, SLC9A8, MAP4K3, TH

HSP40

 

GO:0006950 (adj p-val = 4.0E-05)

HSP47, HSPA8, HSPB2, STUB1, MAPK1, UCP3, HSF1, MAPK14, UNG, SOD1

Wollenberg Valero et al. 2014

Homeostasis

AQP2

 

CHERP, AQP11, SLC9A8, ATP1A1, AQP2

  

GO:0006874 (adj p-val = 0.03); GO:0072503 (adj p-val = 0.04)

LPL, CETP, SCL6A19, ACE2, AGT

Wollenberg Valero et al. 2014; Vianna et al. 2020

Circadian rhythm

CREB1, PHLPP1

 

PROX1, ROCK2, GPR176, ASMT, PTCHD1

 

PHLPP1

 

ADCY2, ADCY8, CALML4, CAMK2

Lin et al. 2019

Phototransduction

  

RGS9, CRB2, MREG, ARR3, TLE4, ABCB5, FOXN4, GRIFIN, SPATA7, ABCA4, CRB1

CRB1

 

GO:0042462 (adj p-val = 0.04)

CNGB1, MYO3A, UACA, CRB1, CRY2, MYO3B

Li et al. 2014

Mitochondrial activity

GLS

GLS

CHCHD6, PTCD3, SLC25A4, VPS13D, SPG20, SERAC1, OPA1, SLC25A3, PNPT1, LRPPRC, GLS

SLC25A3, PNPT1, LRPPRC, GLS

  

COX1, ATP8, ND4L, ND4

Ramos et al. 2018

Temperature sensing

TRPM8

TRPM8

TRPM8

   

TRPM8, TRPV3, TRPV4, TRPA1, TRPM4

Lynch et al. 2015

Membrane fluidity

SGMS2

SGMS2

SGMS2

  

GO:1905371 (adj p-val = 0.04)*

–

This study

  1. Candidate genes under selection in the Emperor penguins which were also found in previous studies are in bold (four genes).
  2. Note that, in the GO ID column, we associated the Gene Ontology Biological Process supported by gProfiler in candidate genes inferred by aBSREL or CODEML (bm), or in the subset of genes inferred by both (marked with *), with relevant biological functions; the GOs in this column do not only refer to the genes indicated in the previous columns. **Weak evidence of gene expression change in a study on feathers development (Ng et al. 2015). Biological function membrane fluidity is proposed herein as related to cold adaptation.
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