-
1
-
-
0031829783
-
RAPDs and allozymes exhibit similar levels of diversity and differentiation among populations and races of Douglas-fir
-
COI: 1:CAS:528:DyaK1cXlsVSgt7Y%3D
-
Aagaard JE, Krutovskii KV, Strauss SH (1998) RAPDs and allozymes exhibit similar levels of diversity and differentiation among populations and races of Douglas-fir. Heredity 81 (1):69–78. 10.1046/j.1365-2540.1998.00355.x
-
(1998)
Heredity
, vol.81
, Issue.1
, pp. 69-78
-
-
Aagaard, J.E.1
Krutovskii, K.V.2
Strauss, S.H.3
-
2
-
-
52049112962
-
Testing for neutrality in samples with sequencing errors
-
PID: 18562660
-
Achaz G (2008) Testing for neutrality in samples with sequencing errors. Genetics 179 (3):1409–1424. 10.1534/genetics.109.104042
-
(2008)
Genetics
, vol.179
, Issue.3
, pp. 1409-1424
-
-
Achaz, G.1
-
3
-
-
26944477031
-
Evolution of genome size in conifers
-
Ahuja MR, Neale DB (2005) Evolution of genome size in conifers. Silvae genetica 54 (3):126–137
-
(2005)
Silvae genetica
, vol.54
, Issue.3
, pp. 126-137
-
-
Ahuja, M.R.1
Neale, D.B.2
-
4
-
-
69749099417
-
Fast model-based estimation of ancestry in unrelated individuals
-
COI: 1:CAS:528:DC%2BD1MXhtFCjsLvL, PID: 19648217
-
Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19 (9):1655–1664. 10.1101/gr.094052.109
-
(2009)
Genome Res
, vol.19
, Issue.9
, pp. 1655-1664
-
-
Alexander, D.H.1
Novembre, J.2
Lange, K.3
-
5
-
-
84919727967
-
-
Alexander DH, Novembre J, Lange K (2013) ADMIXTURE 1.23 Software Manual
-
Alexander DH, Novembre J, Lange K (2013) ADMIXTURE 1.23 Software Manual
-
-
-
-
7
-
-
84878449439
-
RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
-
COI: 1:CAS:528:DC%2BC3sXos12msro%3D, PID: 23551379
-
Arnold B, Corbett-Detig RB, Hartl D, Bomblies K (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol Ecol 22 (11):3179–3190. 10.1111/mec.12276
-
(2013)
Mol Ecol
, vol.22
, Issue.11
, pp. 3179-3190
-
-
Arnold, B.1
Corbett-Detig, R.B.2
Hartl, D.3
Bomblies, K.4
-
8
-
-
78149388939
-
Approximate Bayesian computation in evolution and ecology
-
Beaumont MA (2010) Approximate Bayesian computation in evolution and ecology. Ann. Rev. Ecol. Evol. Syst. 41:379–406. 10.1146/annurev-ecolsys-102209-144621
-
(2010)
Ann. Rev. Ecol. Evol. Syst.
, vol.41
, pp. 379-406
-
-
Beaumont, M.A.1
-
9
-
-
0030467524
-
Evaluating loci for use in the genetic analysis of population structure
-
Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond B 263 (1377):1619–1626. 10.1098/rspb.1996.0237
-
(1996)
Proc R Soc Lond B
, vol.263
, Issue.1377
, pp. 1619-1626
-
-
Beaumont, M.A.1
Nichols, R.A.2
-
10
-
-
33751507060
-
Sequential Monte Carlo p-values
-
Besag J, Clifford P (1991) Sequential Monte Carlo p-values. Biometrika 78 (2):301–304. 10.1093/biomet/78.2.301
-
(1991)
Biometrika
, vol.78
, Issue.2
, pp. 301-304
-
-
Besag, J.1
Clifford, P.2
-
12
-
-
0000190415
-
Genecology of Douglas-fir in a watershed in the Oregon Cascades
-
Campbell RK (1979) Genecology of Douglas-fir in a watershed in the Oregon Cascades. Ecology 60 (5):1036–1050. 10.2307/1936871
-
(1979)
Ecology
, vol.60
, Issue.5
, pp. 1036-1050
-
-
Campbell, R.K.1
-
13
-
-
0001516217
-
Genecology of bud-burst phenology in Douglas-fir: response to flushing temperature and chilling
-
Campbell RK, Sugano AI (1979) Genecology of bud-burst phenology in Douglas-fir: response to flushing temperature and chilling. Bot. Gaz. 140 (2):223–231. 10.1086/337079
-
(1979)
Bot. Gaz.
, vol.140
, Issue.2
, pp. 223-231
-
-
Campbell, R.K.1
Sugano, A.I.2
-
14
-
-
27544482154
-
Genomic regions exhibiting positive selection identified from dense genotype data
-
COI: 1:CAS:528:DC%2BD2MXhtF2itb7K, PID: 16251465
-
Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA (2005) Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 15 (11):1553–1565. 10.1101/gr.4326505
-
(2005)
Genome Res
, vol.15
, Issue.11
, pp. 1553-1565
-
-
Carlson, C.S.1
Thomas, D.J.2
Eberle, M.A.3
Swanson, J.E.4
Livingston, R.J.5
Rieder, M.J.6
Nickerson, D.A.7
-
15
-
-
84861153207
-
abc: an R package for approximate Bayesian computation (ABC)
-
Csilléry K, François O, Blum MGB (2012) abc: an R package for approximate Bayesian computation (ABC). Methods Ecol. Evol. 3 (3):475–479. 10.1111/j.2041-210x.2011.00179.x
-
(2012)
Methods Ecol. Evol.
, vol.3
, Issue.3
, pp. 475-479
-
-
Csilléry, K.1
François, O.2
Blum, M.G.B.3
-
16
-
-
79960405019
-
The variant call format and VCFtools
-
COI: 1:CAS:528:DC%2BC3MXptFCqt7w%3D, PID: 21653522
-
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group (2011) The variant call format and VCFtools. Bioinformatics 27 (15):2156–2158. 10.1093/bioinformatics/btr330
-
(2011)
Bioinformatics
, vol.27
, Issue.15
, pp. 2156-2158
-
-
Danecek, P.1
Auton, A.2
Abecasis, G.3
Albers, C.A.4
Banks, E.5
DePristo, M.A.6
Handsaker, R.E.7
Lunter, G.8
Marth, G.T.9
Sherry, S.T.10
McVean, G.11
Durbin, R.12
1000 Genomes Project Analysis Group13
-
17
-
-
84859935298
-
High levels of RNA-editing site conservation amongst 15 laboratory mouse strains
-
COI: 1:CAS:528:DC%2BC38XptV2jurw%3D, PID: 22524474
-
Danecek P, Nellåker C, McIntyre RE, Buendia-Buendia JE, Bumpstead S, Ponting CP, Flint J, Durbin R, Keane TM, Adams DJ (2012) High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol 13 (4):26. 10.1186/gb-2012-13-4-r26
-
(2012)
Genome Biol
, vol.13
, Issue.4
, pp. 26
-
-
Danecek, P.1
Nellåker, C.2
McIntyre, R.E.3
Buendia-Buendia, J.E.4
Bumpstead, S.5
Ponting, C.P.6
Flint, J.7
Durbin, R.8
Keane, T.M.9
Adams, D.J.10
-
18
-
-
34547944911
-
Genotype and population performances and their interactions for growth of coastal Douglas-fir in western Washington
-
Dean CA (2007) Genotype and population performances and their interactions for growth of coastal Douglas-fir in western Washington. For. Sci. 53 (4):463–472
-
(2007)
For. Sci.
, vol.53
, Issue.4
, pp. 463-472
-
-
Dean, C.A.1
-
19
-
-
45849153848
-
The influence of the ectomycorrhizal fungus Rhizopogon subareolatus on growth and nutrient element localisation in two varieties of Douglas fir (Pseudotsuga menziesii var. menziesii and var. glauca) in response to manganese stress
-
PID: 18437431
-
Ducić T, Parladé J, Polle A (2008) The influence of the ectomycorrhizal fungus Rhizopogon subareolatus on growth and nutrient element localisation in two varieties of Douglas fir (Pseudotsuga menziesii var. menziesii and var. glauca) in response to manganese stress. Mycorrhiza 18 (5):227–239. 10.1007/s00572-008-0174-5
-
(2008)
Mycorrhiza
, vol.18
, Issue.5
, pp. 227-239
-
-
Ducić, T.1
Parladé, J.2
Polle, A.3
-
20
-
-
70350150367
-
Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits
-
COI: 1:CAS:528:DC%2BD1MXhtFGkur7M, PID: 19487566
-
Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, St Clair JB, Neale DB (2009a) Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182 (4):1289–1302. 10.1534/genetics.109.102350
-
(2009)
Genetics
, vol.182
, Issue.4
, pp. 1289-1302
-
-
Eckert, A.J.1
Bower, A.D.2
Wegrzyn, J.L.3
Pande, B.4
Jermstad, K.D.5
Krutovsky, K.V.6
St Clair, J.B.7
Neale, D.B.8
-
21
-
-
70350153315
-
Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas fir (Pseudotsuga menziesii var. menziesii)
-
PID: 19596906
-
Eckert AJ, Wegrzyn JL, Pande B, Jermstad KD, Lee JM, Liechty JD, Tearse BR, Krutovsky KV, Neale DB (2009b) Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas fir (Pseudotsuga menziesii var. menziesii). Genetics 183 (1):289–298. 10.1534/genetics.109.103895
-
(2009)
Genetics
, vol.183
, Issue.1
, pp. 289-298
-
-
Eckert, A.J.1
Wegrzyn, J.L.2
Pande, B.3
Jermstad, K.D.4
Lee, J.M.5
Liechty, J.D.6
Tearse, B.R.7
Krutovsky, K.V.8
Neale, D.B.9
-
22
-
-
0033911640
-
Hitchhiking under positive Darwinian selection
-
COI: 1:STN:280:DC%2BD3cvgsVSntQ%3D%3D, PID: 10880498
-
Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155 (3):1405–1413
-
(2000)
Genetics
, vol.155
, Issue.3
, pp. 1405-1413
-
-
Fay, J.C.1
Wu, C.I.2
-
23
-
-
58149347836
-
A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective
-
PID: 18780740
-
Foll M, Gaggiotti O (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180 (2):977–993. 10.1534/genetics.108.092221
-
(2008)
Genetics
, vol.180
, Issue.2
, pp. 977-993
-
-
Foll, M.1
Gaggiotti, O.2
-
24
-
-
0001783722
-
Étude de la decroissance des valeurs propres dans une analyze en composantes principales: comparison avec le modèle de baton brisé
-
Frontier S (1976) Étude de la decroissance des valeurs propres dans une analyze en composantes principales: comparison avec le modèle de baton brisé. J Exp Marine Biol 25:67–75. 10.1016/0022-0981(76)90076-9
-
(1976)
J Exp Marine Biol
, vol.25
, pp. 67-75
-
-
Frontier, S.1
-
25
-
-
78650486589
-
Molecular footprints of local adaptation in two mediterranean conifers
-
COI: 1:CAS:528:DC%2BC3cXhsF2rsb7O, PID: 20656795
-
Grivet D, Sebastiani F, Alía R, Bataillon T, Torre S, Zabal-Aguirre M, Vendramin GG, González-Martínez SC (2011) Molecular footprints of local adaptation in two mediterranean conifers. Mol Biol Evol 28 (1):101–116. 10.1093/molbev/msq190
-
(2011)
Mol Biol Evol
, vol.28
, Issue.1
, pp. 101-116
-
-
Grivet, D.1
Sebastiani, F.2
Alía, R.3
Bataillon, T.4
Torre, S.5
Zabal-Aguirre, M.6
Vendramin, G.G.7
González-Martínez, S.C.8
-
26
-
-
84858591099
-
Targeted sequence capture as a powerful tool for evolutionary analysis
-
PID: 22268225
-
Grover CE, Salmon A, Wendel JF (2012) Targeted sequence capture as a powerful tool for evolutionary analysis. Am J Bot 99 (2):312–319. 10.3732/ajb.1100323
-
(2012)
Am J Bot
, vol.99
, Issue.2
, pp. 312-319
-
-
Grover, C.E.1
Salmon, A.2
Wendel, J.F.3
-
27
-
-
84883774412
-
Robust identification of local adaptation from allele frequencies
-
PID: 23821598
-
Günther T, Coop G (2013) Robust identification of local adaptation from allele frequencies. Genetics 195 (1):205–220. 10.1534/genetics.113.152462
-
(2013)
Genetics
, vol.195
, Issue.1
, pp. 205-220
-
-
Günther, T.1
Coop, G.2
-
28
-
-
84874601070
-
Climate change may cause severe loss in the economic value of European forest land. Nature Clim Change advance online publication
-
Hanewinkel M, Cullmann DA, Schelhaas MJ, Nabuurs GJ, Zimmermann NE (2012) Climate change may cause severe loss in the economic value of European forest land. Nature Clim Change advance online publication, 10.1038/nclimate1687
-
(2012)
10.1038/nclimate1687
-
-
Hanewinkel, M.1
Cullmann, D.A.2
Schelhaas, M.J.3
Nabuurs, G.J.4
Zimmermann, N.E.5
-
29
-
-
79551699087
-
The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82
-
COI: 1:CAS:528:DC%2BC3MXksFOjsL8%3D, PID: 21115807
-
Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155 (2):645–655. 10.1104/pp.110.166736
-
(2011)
Plant Physiol
, vol.155
, Issue.2
, pp. 645-655
-
-
Haun, W.J.1
Hyten, D.L.2
Xu, W.W.3
Gerhardt, D.J.4
Albert, T.J.5
Richmond, T.6
Jeddeloh, J.A.7
Jia, G.8
Springer, N.M.9
Vance, C.P.10
Stupar, R.M.11
-
30
-
-
84867807525
-
Genome-wide analysis of cis-regulatory divergence between species in the Arabidopsis genus
-
COI: 1:CAS:528:DC%2BC38XhsFCru7vK, PID: 22641789
-
He F, Zhang X, Hu J, Turck F, Dong X, Goebel U, Borevitz J, de Meaux J (2012) Genome-wide analysis of cis-regulatory divergence between species in the Arabidopsis genus. Mol Biol Evol 29 (11):3385–3395. 10.1093/molbev/mss146
-
(2012)
Mol Biol Evol
, vol.29
, Issue.11
, pp. 3385-3395
-
-
He, F.1
Zhang, X.2
Hu, J.3
Turck, F.4
Dong, X.5
Goebel, U.6
Borevitz, J.7
de Meaux, J.8
-
31
-
-
79951759855
-
Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges
-
COI: 1:STN:280:DC%2BC3MzotVaiuw%3D%3D, PID: 21429169
-
Helyar SJ, Hemmer-Hansen J, Bekkevold D, Taylor MI, Ogden R, Limborg MT, Cariani A, Maes GE, Diopere E, Carvalho GR, Nielsen EE (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 11 Suppl 1:123–136. 10.1111/j.1755-0998.2010.02943.x
-
(2011)
Mol Ecol Resour
, vol.11 Suppl 1
, pp. 123-136
-
-
Helyar, S.J.1
Hemmer-Hansen, J.2
Bekkevold, D.3
Taylor, M.I.4
Ogden, R.5
Limborg, M.T.6
Cariani, A.7
Maes, G.E.8
Diopere, E.9
Carvalho, G.R.10
Nielsen, E.E.11
-
32
-
-
84901455676
-
Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing
-
Henry IM, Nagalakshmi U, Lieberman MC, Ngo KJ, Krasileva KV, Vasquez-Gross H, Akhunova A, Akhunov E, Dubcovsky J, Tai TH, Comai L (2014) Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell. 10.1105/tpc.113.121590
-
(2014)
Plant Cell
-
-
Henry, I.M.1
Nagalakshmi, U.2
Lieberman, M.C.3
Ngo, K.J.4
Krasileva, K.V.5
Vasquez-Gross, H.6
Akhunova, A.7
Akhunov, E.8
Dubcovsky, J.9
Tai, T.H.10
Comai, L.11
-
33
-
-
0032803819
-
Douglas-fir planted forests
-
Hermann RK, Lavender DP (1999) Douglas-fir planted forests. New Forest 17:53–70. 10.1023/A:1006581028080
-
(1999)
New Forest
, vol.17
, pp. 53-70
-
-
Hermann, R.K.1
Lavender, D.P.2
-
34
-
-
33845746244
-
Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]
-
COI: 1:CAS:528:DC%2BD2sXhs1Wgt7w%3D, PID: 17057229
-
Heuertz M, De Paoli E, Källman T, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174 (4):2095–2105. 10.1534/genetics.106.065102
-
(2006)
Genetics
, vol.174
, Issue.4
, pp. 2095-2105
-
-
Heuertz, M.1
De Paoli, E.2
Källman, T.3
Larsson, H.4
Jurman, I.5
Morgante, M.6
Lascoux, M.7
Gyllenstrand, N.8
-
35
-
-
84874387232
-
A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation
-
COI: 1:CAS:528:DC%2BC3sXhsVOrtLvK, PID: 23445355
-
Howe GT, Yu J, Knaus B, Cronn R, Kolpak S, Dolan P, Lorenz WW, Dean JFD (2013) A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics 14:137. 10.1186/1471-2164-14-137
-
(2013)
BMC Genomics
, vol.14
, pp. 137
-
-
Howe, G.T.1
Yu, J.2
Knaus, B.3
Cronn, R.4
Kolpak, S.5
Dolan, P.6
Lorenz, W.W.7
Dean, J.F.D.8
-
36
-
-
0036184745
-
Generating samples under a Wright-Fisher neutral model
-
COI: 1:CAS:528:DC%2BD38XitFentrw%3D, PID: 11847089
-
Hudson RR (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337–338. 10.1093/bioinformatics/18.2.337
-
(2002)
Bioinformatics
, vol.18
, pp. 337-338
-
-
Hudson, R.R.1
-
37
-
-
84919727964
-
-
IPCC (2007) Intergovernmental Panel on Climate Change - Fourth Assessment Report
-
IPCC (2007) Intergovernmental Panel on Climate Change - Fourth Assessment Report
-
-
-
-
38
-
-
0027332773
-
Stopping rules in principal components analysis: a comparison of heuristical and statistical approaches
-
Jackson DA (1993) Stopping rules in principal components analysis: a comparison of heuristical and statistical approaches. Ecology 74 (8):2204–2214. 10.2307/1939574
-
(1993)
Ecology
, vol.74
, Issue.8
, pp. 2204-2214
-
-
Jackson, D.A.1
-
39
-
-
77649176976
-
The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evol Biol 10 (1)
-
Jaramillo-Correa JP, Verdú M, González-Martínez SC (2010) The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evol Biol 10 (1). 10.1186/1471-2148-10-22
-
(2010)
10.1186/1471-2148-10-22
-
-
Jaramillo-Correa, J.P.1
Verdú, M.2
González-Martínez, S.C.3
-
40
-
-
44349095887
-
adegenet: a R package for the multivariate analysis of genetic markers
-
COI: 1:CAS:528:DC%2BD1cXmtVais7s%3D, PID: 18397895
-
Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405. 10.1093/bioinformatics/btn129
-
(2008)
Bioinformatics
, vol.24
, pp. 1403-1405
-
-
Jombart, T.1
-
41
-
-
77957919360
-
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
-
PID: 20950446
-
Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94. 10.1186/1471-2156-11-94
-
(2010)
BMC Genet
, vol.11
, pp. 94
-
-
Jombart, T.1
Devillard, S.2
Balloux, F.3
-
43
-
-
84856762186
-
Effects of seed source origin on bark thickness of Douglas-fir (Pseudotsuga menziesii) growing in southwestern Germany
-
Kohnle U, Hein S, Sorensen FC, Weiskittel AR (2012) Effects of seed source origin on bark thickness of Douglas-fir (Pseudotsuga menziesii) growing in southwestern Germany. Can. J. For. Res. 42 (2):382–399. 10.1139/x11-191
-
(2012)
Can. J. For. Res.
, vol.42
, Issue.2
, pp. 382-399
-
-
Kohnle, U.1
Hein, S.2
Sorensen, F.C.3
Weiskittel, A.R.4
-
44
-
-
70349817292
-
Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers
-
Krutovsky K, St Clair J, Saich R, Hipkins V, Neale D (2009) Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers. Tree Genet Genomes 5 (4):641–658. 10.1007/s11295-009-0216-y
-
(2009)
Tree Genet Genomes
, vol.5
, Issue.4
, pp. 641-658
-
-
Krutovsky, K.1
St Clair, J.2
Saich, R.3
Hipkins, V.4
Neale, D.5
-
45
-
-
33645130943
-
Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir
-
COI: 1:CAS:528:DC%2BD28XovVyjsA%3D%3D, PID: 16157674
-
Krutovsky KV, Neale DB (2005) Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir. Genetics 171 (4):2029–2041. 10.1534/genetics.105.044420
-
(2005)
Genetics
, vol.171
, Issue.4
, pp. 2029-2041
-
-
Krutovsky, K.V.1
Neale, D.B.2
-
46
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
PID: 19505943
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25 (16):2078–2079. 10.1093/bioinformatics/btp352
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
1000 Genome Project Data Processing Subgroup10
-
47
-
-
84899624756
-
Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests
-
ST outlier tests. Mol Ecol. 10.1111/mec.12725
-
(2014)
Mol Ecol
-
-
Lotterhos, K.E.1
Whitlock, M.C.2
-
48
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 17 (1):10–12. 10.14806/ej.17.1.200
-
(2011)
EMBnetjournal
, vol.17
, Issue.1
, pp. 10-12
-
-
Martin, M.1
-
49
-
-
84885672827
-
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond
-
COI: 1:CAS:528:DC%2BC3sXhs1Wntb7N, PID: 23889683
-
Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D’Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer K FX, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N (2013) Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J 76 (3):494–505. 10.1111/tpj.12294
-
(2013)
Plant J
, vol.76
, Issue.3
, pp. 494-505
-
-
Mascher, M.1
Richmond, T.A.2
Gerhardt, D.J.3
Himmelbach, A.4
Clissold, L.5
Sampath, D.6
Ayling, S.7
Steuernagel, B.8
Pfeifer, M.9
D’Ascenzo, M.10
Akhunov, E.D.11
Hedley, P.E.12
Gonzales, A.M.13
Morrell, P.L.14
Kilian, B.15
Blattner, F.R.16
Scholz, U.17
Mayer, K.F.X.18
Flavell, A.J.19
Muehlbauer, G.J.20
Waugh, R.21
Jeddeloh, J.A.22
Stein, N.23
more..
-
50
-
-
84868197818
-
Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests
-
COI: 1:CAS:528:DC%2BC3sXnt1KltQ%3D%3D, PID: 23144662
-
Mosca E, Eckert AJ, Liechty JD, Wegrzyn JL, La Porta N, Vendramin GG, Neale DB (2012) Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests. Evol Appl 5 (1):762–775. 10.1111/j.1752-4571.2012.00256.x
-
(2012)
Evol Appl
, vol.5
, Issue.1
, pp. 762-775
-
-
Mosca, E.1
Eckert, A.J.2
Liechty, J.D.3
Wegrzyn, J.L.4
La Porta, N.5
Vendramin, G.G.6
Neale, D.B.7
-
51
-
-
84876975995
-
A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings
-
PID: 23190494
-
Müller T, Ensminger I, Schmid KJ (2012) A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings. BMC Genomics 13 (1):673. 10.1186/1471-2164-13-673
-
(2012)
BMC Genomics
, vol.13
, Issue.1
, pp. 673
-
-
Müller, T.1
Ensminger, I.2
Schmid, K.J.3
-
52
-
-
3042745450
-
Association genetics of complex traits in conifers
-
COI: 1:CAS:528:DC%2BD2cXlsVSnur8%3D, PID: 15231277
-
Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9 (7):325–330. 10.1016/j.tplants.2004.05.006
-
(2004)
Trends Plant Sci
, vol.9
, Issue.7
, pp. 325-330
-
-
Neale, D.B.1
Savolainen, O.2
-
53
-
-
41149124114
-
Population, quantitative and comparative genomics of adaptation in forest trees
-
COI: 1:CAS:528:DC%2BD1cXktFCms78%3D, PID: 18262830
-
Neale DB, Ingvarsson PK (2008) Population, quantitative and comparative genomics of adaptation in forest trees. Curr Opin Plant Biol 11 (2):149–155. 10.1016/j.pbi.2007.12.004
-
(2008)
Curr Opin Plant Biol
, vol.11
, Issue.2
, pp. 149-155
-
-
Neale, D.B.1
Ingvarsson, P.K.2
-
54
-
-
78751550555
-
Forest tree genomics: growing resources and applications
-
COI: 1:CAS:528:DC%2BC3MXmsVelsA%3D%3D, PID: 21245829
-
Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nat Rev Genet 12 (2):111–122. 10.1038/nrg2931
-
(2011)
Nat Rev Genet
, vol.12
, Issue.2
, pp. 111-122
-
-
Neale, D.B.1
Kremer, A.2
-
55
-
-
84883755640
-
Open access to tree genomes: the path to a better forest
-
PID: 23796049
-
Neale DB, Langley CH, Salzberg SL, Wegrzyn JL (2013) Open access to tree genomes: the path to a better forest. Genome Biol 14 (6):120. 10.1186/gb-2013-14-6-120
-
(2013)
Genome Biol
, vol.14
, Issue.6
, pp. 120
-
-
Neale, D.B.1
Langley, C.H.2
Salzberg, S.L.3
Wegrzyn, J.L.4
-
56
-
-
84899103272
-
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
-
PID: 24647006
-
Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, Dejong PJ, Yorke JA, Salzberg SL, Langley CH (2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 15 (3):R59. 10.1186/gb-2014-15-3-r59
-
(2014)
Genome Biol
, vol.15
, Issue.3
, pp. R59
-
-
Neale, D.B.1
Wegrzyn, J.L.2
Stevens, K.A.3
Zimin, A.V.4
Puiu, D.5
Crepeau, M.W.6
Cardeno, C.7
Koriabine, M.8
Holtz-Morris, A.E.9
Liechty, J.D.10
Martínez-García, P.J.11
Vasquez-Gross, H.A.12
Lin, B.Y.13
Zieve, J.J.14
Dougherty, W.M.15
Fuentes-Soriano, S.16
Wu, L.S.17
Gilbert, D.18
Marçais, G.19
Roberts, M.20
Holt, C.21
Yandell, M.22
Davis, J.M.23
Smith, K.E.24
Dean, J.F.25
Lorenz, W.W.26
Whetten, R.W.27
Sederoff, R.28
Wheeler, N.29
McGuire, P.E.30
Main, D.31
Loopstra, C.A.32
Mockaitis, K.33
Dejong, P.J.34
Yorke, J.A.35
Salzberg, S.L.36
Langley, C.H.37
more..
-
57
-
-
85000065831
-
NimbleGen SeqCap EZ Library SR User’s Guide, version 3.0
-
NimbleGen (2011) NimbleGen SeqCap EZ Library SR User’s Guide, version 3.0. Roche NimbleGen
-
(2011)
Roche NimbleGen
-
-
-
58
-
-
84878420758
-
The Norway spruce genome sequence and conifer genome evolution
-
COI: 1:CAS:528:DC%2BC3sXotFSns7g%3D, PID: 23698360
-
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield D G, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497 (7451):579–584. 10.1038/nature12211
-
(2013)
Nature
, vol.497
, Issue.7451
, pp. 579-584
-
-
Nystedt, B.1
Street, N.R.2
Wetterbom, A.3
Zuccolo, A.4
Lin, Y.C.5
Scofield, D.G.6
Vezzi, F.7
Delhomme, N.8
Giacomello, S.9
Alexeyenko, A.10
Vicedomini, R.11
Sahlin, K.12
Sherwood, E.13
Elfstrand, M.14
Gramzow, L.15
Holmberg, K.16
Hällman, J.17
Keech, O.18
Klasson, L.19
Koriabine, M.20
Kucukoglu, M.21
Käller, M.22
Luthman, J.23
Lysholm, F.24
Niittylä, T.25
Olson, A.26
Rilakovic, N.27
Ritland, C.28
Rosselló, J.A.29
Sena, J.30
Svensson, T.31
Talavera-López, C.32
Theißen, G.33
Tuominen, H.34
Vanneste, K.35
Wu, Z.Q.36
Zhang, B.37
Zerbe, P.38
Arvestad, L.39
Bhalerao, R.40
Bohlmann, J.41
Bousquet, J.42
Garcia Gil, R.43
Hvidsten, T.R.44
de Jong, P.45
MacKay, J.46
Morgante, M.47
Ritland, K.48
Sundberg, B.49
Thompson, S.L.50
Van de Peer, Y.51
Andersson, B.52
Nilsson, O.53
Ingvarsson, P.K.54
Lundeberg, J.55
Jansson, S.56
more..
-
59
-
-
56449109597
-
Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps
-
PID: 18775901
-
Palmé AE, Wright M, Savolainen O (2008) Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps. Mol Biol Evol 25 (12):2567–2577. 10.1093/molbev/msn194
-
(2008)
Mol Biol Evol
, vol.25
, Issue.12
, pp. 2567-2577
-
-
Palmé, A.E.1
Wright, M.2
Savolainen, O.3
-
60
-
-
62349127448
-
Selection on nuclear genes in a Pinus phylogeny
-
PID: 19168564
-
Palmé AE, Pyhäjärvi T, Wachowiak W, Savolainen O (2009) Selection on nuclear genes in a Pinus phylogeny. Mol Biol Evol 26 (4):893–905. 10.1093/molbev/msp010
-
(2009)
Mol Biol Evol
, vol.26
, Issue.4
, pp. 893-905
-
-
Palmé, A.E.1
Pyhäjärvi, T.2
Wachowiak, W.3
Savolainen, O.4
-
61
-
-
1042304216
-
APE: analyses of phylogenetics and evolution in R language
-
COI: 1:CAS:528:DC%2BD2cXms1eitg%3D%3D, PID: 14734327
-
Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20 (2):289–290. 10.1093/bioinformatics/btg412
-
(2004)
Bioinformatics
, vol.20
, Issue.2
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
62
-
-
77955653063
-
Genome-wide association studies—data generation, storage, interpretation, and bioinformatics
-
PID: 20560038
-
Pare G (2010) Genome-wide association studies—data generation, storage, interpretation, and bioinformatics. J Cardiovasc Transl Res 3 (3):183–188. 10.1007/s12265-010-9181-y
-
(2010)
J Cardiovasc Transl Res
, vol.3
, Issue.3
, pp. 183-188
-
-
Pare, G.1
-
63
-
-
77954714407
-
msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis
-
COI: 1:STN:280:DC%2BC3MrgslSgtw%3D%3D, PID: 21565078
-
Pavlidis P, Laurent S, Stephan W (2010) msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis. Mol Ecol Resour 10 (4):723–727. 10.1111/j.1755-0998.2010.02832.x
-
(2010)
Mol Ecol Resour
, vol.10
, Issue.4
, pp. 723-727
-
-
Pavlidis, P.1
Laurent, S.2
Stephan, W.3
-
64
-
-
84901282318
-
Speeding up large-scale next generation sequencing data analysis with pBWA
-
Peters D, Luo X, Qiu K, Liang P (2012) Speeding up large-scale next generation sequencing data analysis with pBWA. J Biocomput 1 (1)
-
(2012)
J Biocomput
, vol.1
, Issue.1
-
-
Peters, D.1
Luo, X.2
Qiu, K.3
Liang, P.4
-
65
-
-
34548292504
-
PLINK: a toolset for whole-genome association and population-based linkage analysis
-
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D, Maller J, Sklar P, de Bakker P, Daly M, Sham P (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81. 10.1086/519795
-
(2007)
Am J Hum Genet 81
, vol.1086
, pp. 10
-
-
Purcell, S.1
Neale, B.2
Todd-Brown, K.3
Thomas, L.4
Ferreira, M.5
Bender, D.6
Maller, J.7
Sklar, P.8
de Bakker, P.9
Daly, M.10
Sham, P.11
-
66
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
COI: 1:CAS:528:DC%2BC3cXivFGkurc%3D, PID: 20110278
-
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26 (6):841–842. 10.1093/bioinformatics/btq033
-
(2010)
Bioinformatics
, vol.26
, Issue.6
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
67
-
-
0024879065
-
Ecological adaptations in Douglas-fir (Pseudotsuga menziesii var. glauca): a synthesis
-
Rehfeldt G (1989) Ecological adaptations in Douglas-fir (Pseudotsuga menziesii var. glauca): a synthesis. Forest Ecol Manag 28 (3):203–215. 10.1016/0378-1127(89)90004-2
-
(1989)
Forest Ecol Manag
, vol.28
, Issue.3
, pp. 203-215
-
-
Rehfeldt, G.1
-
68
-
-
0024313579
-
Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism
-
COI: 1:CAS:528:DyaK3cXhslentA%3D%3D, PID: 2513255
-
Tajima F (1989) Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585– 595
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
69
-
-
0034886133
-
Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci
-
COI: 1:CAS:528:DC%2BD3MXltFWjsLg%3D, PID: 11444691
-
Viard F, El-Kassaby YA, Ritland K (2001) Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci. Genome 44 (3):336–344. 10.1139/g01-010
-
(2001)
Genome
, vol.44
, Issue.3
, pp. 336-344
-
-
Viard, F.1
El-Kassaby, Y.A.2
Ritland, K.3
-
70
-
-
85027952695
-
Range-wide chloroplast and mitochondrial DNA imprints reveal multiple lineages and complex biogeographic history for Douglas-fir
-
Wei XX, Beaulieu J, Khasa D, Vargas-Hernández J, López-Upton J, Jaquish B, Bousquet J (2011) Range-wide chloroplast and mitochondrial DNA imprints reveal multiple lineages and complex biogeographic history for Douglas-fir. Tree Genet Genomes 7 (5):1025–1040. 10.1007/s11295-011-0392-4
-
(2011)
Tree Genet Genomes
, vol.7
, Issue.5
, pp. 1025-1040
-
-
Wei, X.X.1
Beaulieu, J.2
Khasa, D.3
Vargas-Hernández, J.4
López-Upton, J.5
Jaquish, B.6
Bousquet, J.7
-
71
-
-
0021566877
-
Estimating F-statistics for the analysis of population structure
-
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38 (1358–1370). 10.2307/2408641
-
(1984)
Evolution 38 (1358–1370)
, vol.2307
, pp. 10
-
-
Weir, B.S.1
Cockerham, C.C.2
-
72
-
-
17644379063
-
A note on exact tests of Hardy-Weinberg equilibrium
-
COI: 1:CAS:528:DC%2BD2MXjs12rtLY%3D, PID: 15789306
-
Wigginton JE, Cutler DJ, Abecasis GR (2005) A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet 76 (5):887–893. 10.1086/429864
-
(2005)
Am J Hum Genet
, vol.76
, Issue.5
, pp. 887-893
-
-
Wigginton, J.E.1
Cutler, D.J.2
Abecasis, G.R.3
-
73
-
-
84899102003
-
Sequencing and assembly of the 22-Gb loblolly pine genome
-
COI: 1:CAS:528:DC%2BC2cXhtl2rs7nK, PID: 24653210
-
Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn J L, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH (2014) Sequencing and assembly of the 22-Gb loblolly pine genome. Genetics 196 (3):875–890. 10.1534/genetics.113.159715
-
(2014)
Genetics
, vol.196
, Issue.3
, pp. 875-890
-
-
Zimin, A.1
Stevens, K.A.2
Crepeau, M.W.3
Holtz-Morris, A.4
Koriabine, M.5
Marçais, G.6
Puiu, D.7
Roberts, M.8
Wegrzyn, J.L.9
de Jong, P.J.10
Neale, D.B.11
Salzberg, S.L.12
Yorke, J.A.13
Langley, C.H.14
|