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. 2014 Jun 18;204(1):215–229. doi: 10.1111/nph.12896

Table 4.

Summary of putative adaptive candidates detected across multiple methods in at least one of three subsets of data: lodgepole pine (Pinus contorta var. latifolia), jack pine (Pinus banksiana), and combined, including diversity measures (observed heterozygosity (HO), expected heterozygosity (UHE), and fixation index (F)), their estimated linkage group, the number of positive outlier tests for each data set, the direction of selection, the putative amino acid (AA) change (I, intragenic; NC, noncoding; NS, nonsynonymous; S, synonymous), and their putative annotation

Locus Lodgepole pine Jack pine Linkage group Outlier detection Introgress P-value Direction AA change Annotation
N Ho UHe F N Ho UHe F Combined Lodgepole Jack
JpLpc45225p571 368 0.043 0.043 −0.022 99 0.202 0.183 −0.112 LP07 1 3 0.002 Positive NS B-cell receptor-associated protein 31-like
Lodgc1087p211 368 0.239 0.270 0.112 100 0.000 0.000 LP13 1 3 0.005 Positive NS Proteasome alpha type 7
Lodgc2304p514 367 0.240 0.274 0.123 100 0.010 0.010 −0.005 LP14 1 3 0.240 Positive NS Triosephosphate isomerase
Jp_c01249p362 349 0.610 0.425 −0.439 93 0.516 0.466 −0.113 JP03 2 0.000 Negative NC Short-chain dehydrogenase-reductase B/KR domain
Jp_c21224p439 368 0.402 0.381 −0.057 100 0.350 0.351 −0.004 2 0.547 Negative S Transketolase/dehydrogenase-5-phosphate synthase
Jp_c25075p377 368 0.416 0.419 0.005 100 0.560 0.451 −0.248 2 0.000 Negative S Phenylcoumaran benzylic ether reductase/ NmrA-negative transcriptional regulator
JpLpc33893p239 368 0.016 0.016 −0.008 100 0.070 0.104 0.327 3 0.585 Positive NC Auxin-F-box protein 5
JpLpc41319p340 368 0.027 0.032 0.153 100 0.030 0.049 0.385 2 1 0.992 Positive NC Uncharacterized BCR, YbaB family COG0718
JpLpc47089p1831 366 0.016 0.016 −0.008 100 0.190 0.173 −0.105 2 1 0.249 Positive NC Dof-type zinc finger DNA-binding family protein
JpLpc63491p915 368 0.019 0.019 −0.010 100 0.240 0.256 0.059 2 1 0.002 Positive NC Cytokinin response factor/AP2 domain
JpLpc66545p1207 368 0.019 0.019 −0.010 99 0.081 0.078 −0.042 2 1 0.020 Positive S Transcribed locus
Lp_c00150p459 367 0.014 0.014 −0.007 100 0.130 0.173 0.244 2 0.353 Positive I Circadian clock associated 1
Lodgc118p350 365 0.427 0.467 0.083 100 0.010 0.010 −0.005 LP13 2 3 0.000 Positive S Sedoheptulose-bisphosphate/fructose-1-6-bisphosphate – chloroplast like
Jp_c13093p749 364 0.025 0.024 −0.013 100 0.550 0.496 −0.113 LP04/JP11 2 0.001 Positive NC HSP20-like chaperones superfamily protein
Jp_c13875p1478 367 0.071 0.068 −0.037 LP05 2 na Positive S Pectin methylesterase
Jp_c23409p668 368 0.024 0.024 −0.012 100 0.560 0.499 −0.127 2 0.205 Positive S Glyoxalase/bleomycin resistance protein/dioxygenase superfamily
Jp_c24821p611 368 0.027 0.027 −0.014 100 0.320 0.284 −0.134 1 2 0.494 Positive S Nodulin MtN3 family protein
Jp_c43213p458 368 0.019 0.019 −0.010 100 0.900 0.499 −0.812 LP07 2 0.000 Positive S Lipid transfer protein/seed storage 25 albumin superfamily protein
Jp_c44637p536 368 0.022 0.022 −0.011 100 0.470 0.502 0.059 LP07 2 0.579 Positive NC Coatomer alpha subunit/glycine-rich protein
Jp_c44933p494 368 0.024 0.024 −0.012 100 0.390 0.410 0.043 1 2 0.139 Positive S Photosystem II reaction center protein
JpLpc15608p1838 337 0.151 0.140 −0.082 3 na Positive NC Transducin family protein/WD-40 repeat family protein
JpLpc21364p981 368 0.052 0.056 0.069 100 0.140 0.131 −0.075 1 3 0.000 Positive S myb-like DNA binding domain
JpLpc44782p470 368 0.022 0.022 −0.011 100 0.320 0.297 −0.084 1 2 0.335 Positive S KNOX1/2 domain/KNOTTED-like
Lp_c04318p2154 368 0.207 0.215 0.038 100 0.000 0.000 LP14 3 0.267 Positive NC Carbohydrate binding molecule/starch branching enzyme 2.2
Jackc1504p209 368 0.003 0.003 −0.001 100 0.300 0.309 0.025 2 0.002 Positive S Transcribed locus
Jp_c28904p670 368 0.011 0.011 −0.005 100 0.350 0.488 0.279 2 0.000 Positive NC Ubiquitin-conjugating enzyme 28//E3 interaction residues
Jp_c34152p781 347 0.127 0.124 −0.024 99 0.515 0.502 −0.031 2 0.018 Positive S Ribosomal protein L27
Lodgc6568p554 368 0.329 0.366 0.100 100 0.100 0.131 0.232 JP09 2 0.010 Positive S Flavanone 3-hydroxylase

Bold values indicate P-values that are significant following correction for FDR. na, not available.