Skip to main content

Table 3 Divergent selection constraint parameters estimation and likelihood scores for eight MCPH genes on different partition of mammalian phylogeny

From: Molecular evolutionary analysis of human primary microcephaly genes

Gene

Model

Parameter estimation (ω)

lnL

P value

q value

CEP135

CmC-Primate

p0 = 0.560, ω0 = 0.0231, p1 = 0.142,ω1 = 1.0, p2 = 0.298, ωnp = 0.251, ωp = 0.315

− 26,080.0893

0.057

0.34

CmC-Simians

p0 = 0.296, ω0 = 0.27, p1 = 0.141, ω1 = 1.0, p2 = 0.56, ωns = 0.023, ωs = 0.021

− 26,081.8471

0.75

0.66

CmC-catarrhini

p0 = 0.293, ω0 = 0.271, p1 = 0.141, ω1 = 1.0, p2 = 0.57, ωnc = 0.023, ωc = 0.0397

− 26,081.3823

0.31

0.58

CmC-greatapes

p0 = 0.295, ω0 = 0.269, p1 = 0.141, ω1 = 1.0, p2 = 0.564, ωng = 0.0235, ωg = 0.0184

− 26,081.8801

0.85

0.66

CmC-hominini

p0 = 0.56, ω0 = 0.023 p1 = 0.141, ω1 = 1.0, p2 = 0.296, ωnh = 0.27, ωh = 0.59

− 26,081.1383

0.22

0.57

M2a_rel

p0 = 0.295, ω0 = 0.269, p1 = 0.0141, ω1 = 1.0, p2 = 0.564, ω2 = 0.0235

− 26,081.8982

NA

NA

ZNF335

CmC-Primate

p0 = 0.75, ω0 = 0.015, p1 = 0.029, ω1 = 1.0, p2 = 0.221, ωnp = 0.255, ωp = 0.285

− 32,294.0420

0.30

0.58

CmC-simians

p0 = 0.751, ω0 = 0.0155, p1 = 0.029, ω1 = 1.0, p2 = 0.22, ωns = 0.256, ωs = 0.312

− 32,293.5981

0.16

0.57

CmC-catarrhini

p0 = 0.751, ω0 = 0.0154, p1 = 0.029, ω1 = 1.0, p2 = 0.22, ωnc = 0.266, ωc = 0.27

− 32,293.5586

0.15

0.57

CmC-greatapes

p0 = 0.75, ω0 = 0.0154, p1 = 0.029, ω1 = 1.0, p2 = 0.22, ωng = 0.259, ωg = 0.297

− 32,294.4826

0.66

0.66

CmC-hominini

p0 = 0.75, ω0 = 0.0154, p1 = 0.029, ω1 = 1.0, p2 = 0.22, ωnh = 0.26, ωh = 0.25

− 32,294.5720

0.92

0.69

M2a_rel

p0 = 0.75, ω0 = 0.015, p1 = 0.029, ω1 = 1.0, p2 = 0.221, ω2 = 0.26

− 32,294.5769

NA

NA

PHC1

CmC-Primate

p0 = 0.784, ω0 = 0.020, p1 = 0.021, ω1 = 1.0, p2 = 0.195, ωnp = 0.339, ωp = 0.395

− 20,737.4013

0.29

0.58

CmC-simians

p0 = 0.194, ω0 = 0.348, p1 = 0.021, ω1 = 1.0, p2 = 0.78, ωns = 0.020, ωs = 0.018

− 20,737.9248

0.82

0.66

CmC-catarrhini

p0 = 0.78, ω0 = 0.020, p1 = 0.021, ω1 = 1.0, p2 = 0.19, ωnc = 0.347, ωc = 0.364

− 20,737.9367

0.86

0.66

CmC-greatapes

p0 = 0.78, ω0 = 0.020, p1 = 0.021, ω1 = 1.0, p2 = 0.19, ωng = 0.349, ωg = 0.179

− 20,737.3879

0.29

0.58

CmC-hominini

p0 = 0.78, ω0 = 0.020, p1 = 0.021, ω1 = 1.0, p2 = 0.19, ωnh = 0.35, ωh = 0.13

− 20,737.5787

0.38

0.65

M2a_rel

p0 = 0.784, ω0 = 0.020, p1 = 0.021, ω1 = 1.0, p2 = 0.194, ω2 = 0.348

− 20,737.9512

NA

NA

SASS6

CmC-Primate

p0 = 0.612, ω0 = 0.017, p1 = 0.077, ω1 = 1.0, p2 = 0.310, ωnp = 0.253, ωp = 0.270

− 14,706.9216

0.67

0.66

CmC-simians

p0 = 0.58, ω0 = 0.013, p1 = 0.082, ω1 = 1.0, p2 = 0.34, ωns = 0.214, ωs = 0.499

− 14,697.4440

0.00001

0.0003

CmC-catarrhini

p0 = 0.31, ω0 = 0.26, p1 = 0.077, ω1 = 1.0, p2 = 0.62, ωnc = 0.017, ωc = 0.024

− 14,706.9516

0.72

0.66

CmC-greatapes

p0 = 0.61, ω0 = 0.17, p1 = 0.078, ω1 = 1.0, p2 = 0.31, ωng = 0.25, ωg = 0.47

− 14,706.3050

0.23

0.57

CmC-hominini

p0 = 0.62, ω0 = 0.017, p1 = 0.077, ω1 = 1.0, p2 = 0.31, ωnh = 0.26, ωh = 1.082

− 14,705.0071

0.045

0.33

M2a_rel

p0 = 0.614, ω0 = 0.017, p1 = 0.077, ω1 = 1.0, p2 = 0.308, ω2 = 0.259

− 14,707.0141

NA

NA

CDK6

CmC-Primate

p0 = 0.895, ω0 = 0.011, p1 = 0.012, ω1 = 1.0, p2 = 0.0926, ωnp = 0.298, ωp = 0.257

− 5156.14749

0.76

0.66

CmC-Simians

p0 = 0.897, ω0 = 0.012, p1 = 0.014, ω1 = 1.0, p2 = 0.088, ωns = 0.271, ωs = 0.428

− 5155.82423

0.39

0.65

CmC-catarrhini

p0 = 0.902, ω0 = 0.012, p1 = 0.011, ω1 = 1.0, p2 = 0.087, ωnc = 0.32, ωc = 0.16

− 5156.01860

0.55

0.66

CmC-greatapes

p0 = 0.089, ω0 = 0.298, p1 = 0.012, ω1 = 1.0, p2 = 0.899, ωng = 0.012, ωg = 0.00

− 5156.08170

0.63

0.66

CmC-hominini

p0 = 0.089, ω0 = 0.296, p1 = 0.012, ω1 = 1.0, p2 = 0.898, ωnh = 0.012, ωh = 0.00

− 5156.12730

0.71

0.66

M2a_rel

p0 = 0.897, ω0 = 0.011, p1 = 0.012, ω1 = 1.0, p2 = 0.0906, ω2 = 0.294

− 5156.19494

NA

NA

MFSD2A

CmC-Primate

p0 = 0.731, ω0 = 0.0152, p1 = 0.062, ω1 = 1.0, p2 = 0.207, ωnp = 0.257, ωp = 0.279

− 11,299.7769

0.66

0.66

CmC-simians

p0 = 0.719, ω0 = 0.014, p1 = 0.066, ω1 = 1.0, p2 = 0.21, ωns = 0.23, ωs = 0.38

− 11,297.2803

0.02

0.30

CmC-catarrhini

p0 = 0.725, ω0 = 0.015, p1 = 0.065, ω1 = 1.0, p2 = 0.21, ωnc = 0.25, ωc = 0.33

− 11,299.5559

0.43

0.66

CmC-greatapes

p0 = 0.73, ω0 = 0.015, p1 = 0.062, ω1 = 1.0, p2 = 0.21, ωng = 0.262, ωg = 0.289

− 11,299.8560

0.85

0.66

CmC-hominini

p0 = 0.73, ω0 = 0.015, p1 = 0.061, ω1 = 1.0, p2 = 0.21, ωnh = 0.266, ωh = 0.196

− 11,299.8222

0.75

0.66

M2a_rel

p0 = 0.732, ω0 = 0.0154, p1 = 0.061, ω1 = 1.0, p2 = 0.206, ω2 = 0.265

-11,299.8738

NA

NA

CIT

CmC-Primate

p0 = 0.89, ω0 = 0.0058, p1 = 0.014, ω1 = 1.0, p2 = 0.095, ωnp = 0.24, ωp = 0.19

− 35,246.2438

0.18

0.57

CmC-simians

p0 = 0.095, ω0 = 0.226, p1 = 0.015, ω1 = 1.0, p2 = 0.89, ωns = 0.0059, ωs = 0.0043

− 35,246.9740

0.57

0.66

CmC-catarrhini

p0 = 0.094, ω0 = 0.227, p1 = 0.015, ω1 = 1.0, p2 = 0.89, ωnc = 0.0057, ωc = 0.0088

− 35,246.8939

0.49

0.66

CmC-greatapes

p0 = 0.89, ω0 = 0.0058, p1 = 0.015, ω1 = 1.0, p2 = 0.094, ωng = 0.2279, ωg = 0.2074

− 35,247.1167

0.86

0.66

CmC-hominini

p0 = 0.89, ω0 = 0.0057, p1 = 0.015, ω1 = 1.0, p2 = 0.095, ωnh = 0.224, ωh = 0.379

− 35,246.9556

0.55

0.66

M2a_rel

p0 = 0.89, ω0 = 0.0058, p1 = 0.015, ω1 = 1.0, p2 = 0.095, ω2 = 0.227

− 35,247.1321

NA

NA

KIF14

CmC-Primate

p0 = 0.43, ω0 = 0.043, p1 = 0.15, ω1 = 1.0, p2 = 0.42, ωnp = 0.36, ωp = 0.39

− 31,056.0434

0.58

0.66

CmC-simians

p0 = 0.43, ω0 = 0.043, p1 = 0.14, ω1 = 1.0, p2 = 0.42, ωns = 0.36, ωs = 0.42

− 31,055.4805

0.23

0.57

CmC-catarrhini

p0 = 0.43, ω0 = 0.042, p1 = 0.15, ω1 = 1.0, p2 = 0.42, ωnc = 0.36, ωc = 0.41

− 31,055.9687

0.50

0.66

CmC-greatapes

p0 = 0.42, ω0 = 0.37, p1 = 0.15, ω1 = 1.0, p2 = 0.43, ωng = 0.042, ωg = 0.13

− 31,054.6979

0.083

0.42

CmC-hominini

p0 = 0.42, ω0 = 0.37, p1 = 0.15, ω1 = 1.0, p2 = 0.43, ωnh = 0.042, ωh = 0.25

− 31,053.9072

0.03

0.30

M2a_rel

p0 = 0.42, ω0 = 0.37, p1 = 0.15, ω1 = 1.0, p2 = 0.43, ω2 = 0.043

− 31,056.1959

NA

NA

  1. lnL log likelihood score, ω ratio of non-synonymous (dN) to synonymous (dS) substitutions rate, p proportion of sites, NA not applicable, np non-primate eutherian, p primate, ns non-simians eutherian, s simians, nc non-catarrhini eutherian, c catarrhini, ng non-greatapes eutherian, g greatapes, nh non-hominini eutherian, h hominini. Significant p and q values are highlighted in bold