Table 1 SNPs with potential for adaptive selection based on Bayes factor for bioclimatic variables (BF > 10 for at least one bioclimatic 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 Bio04

ρ Bio04

BF Bio05

ρ Bio05

BF Bio16

ρ Bio16

BF Bio17

ρ Bio17

Affected gene

Annotation

Function and SNPEff annotation

D

NKXS01007262

727

1.20E+191

0.16981

1.48E+130

-0.1249

2.41E+200

-0.2012

3.07E+21

-0.0519

  

intergenic_region|MODIFIER

D-

NKXS01007262-

754

4.15E+123

0.13618

4.10E+75

-0.0941

1.78E+170

-0.1606

3.59E+15

-0.0982

Haimp10041442m.g

PF00006

ATP synthase alpha/beta family, nucleotide-binding domainupstream_gene_variant|MODIFIER-

A

NKXS01005069

42043

983440000.0

-0.19315

5047700.0

0.1315

2818.80

0.1489

0.0803

0.0218

Haimp10032484m.g

GO:0008270

zinc ion binding downstream_gene_variant|MODIFIER

A

NKXS01000550

14775

1257900.0

-0.15949

11.9500

0.0974

21362000.0

0.1447

0.1058

0.0371

Haimp10033596m.g

GO:0007094

mitotic spindle assembly checkpoint intron_variant|MODIFIER

C

NKXS01007262

851

110.9500

0.12024

3.6660

-0.1267

402.880

-0.1650

0.1148

0.0224

Haimp10041442m.g

PF00006

ATP synthase alpha/beta family, nucleotide-binding domainsynonymous_variant|LOW-

E

NKXS01009478

3168

85.7210

-0.15862

4.6344

0.0933

8.5058

0.1298

0.1482

0.0078

Haimp10004827m.g

KOG2451

Aldehyde dehydrogenase synonymous_variant|LOW

F

NKXS01008263

19989

2.5250

-0.14615

0.7613

0.1759

17.8370

0.1505

0.0619

-0.0827

Haimp10001090m.g

GO:0004222

metalloendopeptidase activity intron_variant|MODIFIER

F

NKXS01007262

861

0.6732

0.12689

0.1251

-0.1304

1091.00

-0.1522

0.0693

0.0198

Haimp10041442m.g

PF00006

ATP synthase alpha/beta family, nucleotide-binding domainsynonymous_variant|LOW

B

NKXS01000006

391845

0.4059

0.018537

10.0000

0.1240

2.2507

0.0518

27.8500

-0.2410

Haimp10035708m.g

GO:0016760

cellulose synthase (UDP-forming) activityintron_variant|MODIFIER

B

NKXS01001400

41404

0.22740

0.023626

0.1911

0.0867

0.0792

0.0580

13.9020

-0.2358

Haimp10009243m.g

-

intron_variant|MODIFIER

B

NKXS01004138

63677

0.13580

-0.072007

0.0908

0.0667

0.1458

0.0983

46.7970

-0.1984

 

-

intergenic_region|MODIFIER|

B

NKXS01000489

3109

0.1340

0.02834

0.0857

0.0877

0.1449

0.0572

10.3300

-0.2775

Haimp10030846m.g

PF13432

Tetratricopeptide repeat intron_variant|MODIFIER

B

NKXS01002703

64696

0.1118

0.035165

0.0735

0.0752

0.0528

0.0564

14.8830

-0.2750

Haimp10019312m.g

GO:0006777

Mo-molybdopterin cofactor biosynthetic processmissense_variant|MODERATE

A

NKXS01006685

6558

0.0851

0.050983

0.1122

0.0569

0.0775

0.0311

56.6910

-0.2467

Haimp10039384m.g

PF00134

Cyclin, N-terminal domain intron_variant|MODIFIER

C

NKXS01003261

39765

0.0825

0.038259

0.0903

0.0468

0.0548

0.0041

23.1460

-0.1953

Haimp10022642m.g

GO:0016597

amino acid binding synonymous_variant|LOW

E

NKXS01002889

3697

0.0743

0.0009

0.0772

0.0771

0.0616

0.0558

18.6630

-0.1678

Haimp10020435m.g

K15747

cytochrome P450, family 97, subfamily A (beta-ring hydroxylase) ynonymous_variant|LOW

F

NKXS01006483

53149

0.0743

0.0371

0.1034

0.0814

0.0582

0.0379

13.3330

-0.2314

Haimp10038613m.g

GO:0005525

GTP binding upstream_gene_variant|MODIFIER

F

NKXS01008537

7108

0.0738

0.0231

0.0539

0.0809

0.0648

0.0344

34.3730

-0.2197

Haimp10001901m.g

PF04051

Transport protein particle (TRAPP) componentdownstream_gene_variant|MODIFIER

F

NKXS01003977

34289

0.0716

0.0441

0.0657

0.0222

0.1987

0.0142

90.3930

-0.1536

Haimp10026773m.g

GO:0016773

phosphotransferase activity, alcohol group as acceptorintron_variant|MODIFIER

C

NKXS01009331

5768

0.0655

0.0254

0.0572

0.0723

0.0533

0.0643

35.9380

-0.2264

Haimp10004318m.g

GO:0005524

ATP-binding missense_variant|MODERATE

C

NKXS01000816

49036

0.0574

0.0355

0.0614

0.0868

0.0524

0.0424

10.1320

-0.2472

Haimp10042856m.g

PF01256

Carbohydrate kinase intron_variant|MODIFIER

  1. Scaffold, SNP position, and affected gene were obtained from the genome assembly and annotation (Silva-Junior et al. 2018a, 2018b). Class corresponds to the allele frequency class in Fig. 3. Bio4, temperature seasonality; Bio5, maximum temperature of the warmest month; Bio16, precipitation of the wettest quarter; Bio17, precipitation of driest quarter. 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