Table 4 Loci with genomic clines that differ significantly from neutral expectation of introgression

From: Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian non-sister parrot species, Platycercus adscitus and Platycercus eximius

δ ≥ 0.8

Including all individuals (N = 77)

Excluding individuals with high missing data, P. a. adscitus, and hybrid P. adscitus individuals (N = 46)

Locus ID

Delta

LnL

P (α = 0.009)

P(BH)

Genotypes

Delta

LnL

P (α = 0.009)

P(BH)

Genotypes

12901

0.9865

5.8906

0.0165

0.1791

AA Aa aa−

1.0000

6.55182606

0.0075

0.096

AA Aa aa−

14103

0.8676

8.3584

0.0010

0.0304

AA Aa− aa+

NA

NA

NA

NA

NA

33436

1.0000

10.8360

0

0

AA Aa aa−

1.0000

9.8434

0

0

AA Aa aa−

43439

0.9111

13.0684

0

0

AA + Aa aa−

0.8625

13.6749

0

0

AA + Aa aa−

44487

0.9861

6.9197

0.0030

0.0651

AA− Aa + aa

0.9375

6.3849

0.0100

0.1164

AA− Aa + aa

51727

0.9331

8.1617

0.0010

0.0304

AA Aa + aa−

0.8918

8.3633

0.0020

0.0427

AA Aa + aa−

62103

0.8158

7.7701

0.0020

0.0507

AA Aa aa+

0.8333

8.5852

0.0020

0.0427

AA Aa aa+

62567

0.9861

7.0687

0.0040

0.0676

AA− Aa aa+

NA

NA

NA

NA

NA

62645

0.9342

7.5840

0.0040

0.0676

AA− Aa + aa

1.0000

10.7289

0

0

AA Aa aa

80497

0.8462

8.6974

0.0005

0.0253

AA Aa + aa−

0.8889

8.8207

0.0005

0.0160

AA Aa + aa−

82549

0.9861

6.2762

0.0165

0.1791

AA Aa aa

0.9375

7.4709

0.0060

0.0853

AA Aa aa−

92993

NA

NA

NA

NA

NA

0.8493

7.6027

0.0045

0.0823

AA Aa aa

δ = 1

Including all individuals (N = 77)

Excluding individuals with high missing data, P. a. adscitus, and hybrid P. adscitus individuals (N = 46)

Locus ID

Delta

LnL

P (α = 0.013)

P(BH)

Genotypes

Delta

LnL

P (α = 0.011)

P(BH)

Genotypes

12901

NA

NA

NA

NA

NA

1

7.8285757

0.0005

0.00833333

AA Aa aa−

33436

1

11.8203184

0

0

AA Aa + aa−

1

9.6335869

0

0

AA Aa + aa−

62645

NA

NA

NA

NA

NA

1

12.4431847

0

0

AA− Aa + aa

  1. ‘Locus ID’ refers to the Catalogue ID output from denovo_map. ‘Delta’ indicates the interspecies allele frequency differential. ‘LnL’ refers to the likelihood ratio. ‘P’ signifies the uncorrected probability of departure from neutrality, with α adjusted following the B–Y false discovery rate adjustment procedure described in Narum (2006). ‘P (BH)’ refers to the probability of departure from neutrality following false discovery rate correction (Benjamini and Hockber 1995) using the p.adjust R function. Genotypes indicates the overrepresentation (+) or underrepresentation (−) of observed genotypes
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