Table 2 SNPs with potential for adaptive selection based on Bayes factor for soil variables (BF > 10 for at least one soil variable) and correlation (Spearman’s correlation, |ρ| > 0.15) using Bayenv2 software

From: A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree

Class

Genbank accession

SNP position

BF CEC Clay

ρ CEC Clay

BF CaCO3

ρ CaCO3

BF BS

ρ BS

Affected gene

Annotation

Function and SNPEff annotation

A

NKXS01002061

42170

148.7100

-0.1901

0.3061

-0.0591

1.6204

-0.0417

Haimp10014748m.g

PF00271

Helicase conserved C-terminal domain missense_variant|MODERATE

A

NKXS01001803

112707

47.5550

-0.1633

0.2172

-0.0440

0.2861

-0.0277

Haimp10012826m.g

GO:0016773

Phosphotransferase activity, alcohol group as acceptor synonymous_variant|LOW|

B

NKXS01001173

15335

11.4750

-0.1874

0.2047

-0.0198

0.7671

-0.0298

Haimp10006371m.g

GO:0042626

ATPase activity, coupled to transmembrane movement of substances synonymous_variant|LOW|

C

NKXS01005306

29967

2.2584

0.0246

1.90E + 70

-0.0757

3.95E + 19

-0.1690

Haimp10033515m.g

KOG0032

Ca2 + /calmodulin-dependent protein kinase, EF-hand protein superfamily intron_variant|MODIFIER

D

NKXS01001780

62713

0.1414

-0.0079

2.90E + 53

-0.1708

1.17E + 39

-0.0445

Haimp10012617m.g

KOG1187

Serine/threonine protein kinase synonymous_variant|LOW

D

NKXS01000585

262912

0.1279

0.0096

39.3780

-0.1733

3.6111

-0.1007

Haimp10035204m.g

GO:0016616

Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor intron_variant|MODIFIER

E

NKXS01005306

29965

0.0961

0.0262

1.26E + 128

-0.1006

3.03E + 55

-0.1861

Haimp10033515m.g

KOG0032

Ca2 + /calmodulin-dependent protein kinase, EF-hand protein superfamily intron_variant|MODIFIER

F

NKXS01001446

39931

0.0821

-0.0725

0.5758

-0.1348

13.7060

-0.1516

Haimp10009670m.g

KOG2495

NADH dehydrogenase (ubiquinone) downstream_gene_variant|MODIFIER

F

NKXS01002564

31451

0.0806

-0.0802

16.8870

0.1048

84.9890

0.1741

Haimp10018368m.g

PF01429

Methyl CpG-binding domain intron_variant|MODIFIER

B

NKXS01002428

1817

0.0630

0.0669

2.21E + 114

-0.0933

4.92E + 56

-0.1661

Haimp10017457m.g

PTHR10996

2-Hydroxyacid dehydrogenase-related intron_variant|MODIFIER|

C

NKXS01002564

35233

0.0542

0.0013

2.64E + 43

-0.1935

5.32E + 18

-0.1047

Haimp10018369m.g

KOG2253

U1 snRNP complex subunit SNU71 and related PWI-motif proteins downstream_gene_variant|MODIFIER

  1. Scaffold, SNP position, and affected gene were obtained from the genome assembly and annotation (Silva-Junior et al. 2018a). Class corresponds to the allele frequency class in Fig. 3. CEC Clay, subsoil clay cationic exchange capacity; CACO3, subsoil clay calcium carbonate; BS, subsoil base saturation. SNPEff annotation identifies the SNP position with respect to the genes annotated in the H. impetiginosus genome. Upstream and downstream variants are within 5 kb of the transcribed gene regions
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