Table likelihood values and parameter estimates for the Leptin exon 3




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Table S5. Likelihood values and parameter estimates for the Leptin exon 3 (46 species, 110 aa).


Model/Likelihood ratio test (LRT)

Estimates of Parameters



2Δℓ

df

P-value

Positively selected sites

M0: one-ratio

ω=0.294

-4313.38

-

-

-

None

Free-ratio

variable ω by branch

-4223.34

-

-

-

Not allowed

Site-specific models



















M1a: NearlyNeutral (K=2)

p0=0.684, (p1=0.316)

-4269.73

-

-

-

Not allowed

M2a: Positive selection (K=3)

p0=0.684, p1=0.255, (p2=0.061) (ω0=0.175, ω1=1.000), ω2=0.999

-4269.73

-

-

-

None

M3: discrete (K=3)

p0=0.284, p1=0.399, (p2=0.317) ω0=0.038, ω1=0.250, ω2=0.643

-4247.48

-

-

-

None

M8a: fix omega=1

P=0.767, q=1.640

-4247.68

-

-

-

None

M8: beta&ω>1

p0=1.000, p=0.772, q=1.655, (p1=0.000), ω=1.000

-4247.70

-

-

-

None

Branch-specific model (Two-ratio)



















Chiroptera lineage

ω0= 0.2912, ω1= 1.8494

-4312.54

-

-

-

Not allowed

Yangochiroptera lineage

ω0= 0.2914, ω1= 1.3581

-4312.43

-

-

-

Not allowed

Rhinolophoidea lineage

ω0= 0.2830, ω1= 999.0000

-4305.08

-

-

-

Not allowed

Primate lineage

ω0= 0.2942, ω1= 0.2950

-4313.38

-

-

-

Not allowed

Strepsirrhini lineage

ω0= 0.2942, ω1= 0.2950

-4313.11

-

-

-

Not allowed

Hominid lineage

ω0= 0.2925, ω1= 0.7199

-4309.52

-

-

-

Not allowed

Branch-site models



















Model A

p0= 0.3013, p1= 0.1339, ( p2+p3= 0.5648) (ω0= 0.1679, ω1= 1.0000), ω2=1.3552

-4266.66

-

-

-

3V, 7K, 16P, 19P, 41P, 44N, 61V, 65K, 75L, 85A

Model A’

p0= 0.2376, p1= 0.1059, ( p2+p3= 0.6565) (ω0= 0.1679, ω1= 1.0000), ω2=1.0000

-4266.72

-

-

-

None

LRT of variable ω values among sites



















M0 vs. M3

-

-

131.8

4

<0.001

-

M1a vs. M2a

-

-

0

2

>0.05

-

M8a vs. M8

-

-

0.36

1

>0.05

-

LRT of variable ω values among branches



















Free-ratio vs. M0

-

-

129.86

60

<0.001

-

LRT of ω at specific lineages (one ratio vs. two ratio)



















Chiroptera lineage

-

-

1.68

1

>0.05

-

Yangochiroptera lineage

-

-

1.9

1

>0.05

-

Rhinolophoidea lineage

-

-

16.6

1

<0.001

-

Primate lineage

-

-

0

1

>0.05

-

Strepsirrhini lineage

-

-

0.54

1

>0.05

-

Hominid lineage

-

-

7.72

1

<0.01

-

LRT of variable ω along homeothermic bat lineages



















Model 1a vs. Model A (test I)







5.8

1

<0.05

-

Model A’ vs. Model A (test II)







0.14

1

>0.05

-
ω: dN/dS ratio. ℓ: Log-likelihood ratio. Those in parentheses are presented for clarity only but are not free parameters. Positively selected sites are located with Human Leptin complete CDS as reference and gaps are removed.



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