-
1
-
-
33846839390
-
Bayesian estimation of concordance among gene trees
-
ANÉ, C., B. LARGET, D. A. BAUM, S. D. SMITH, and A. ROKAS. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24: 412-426.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 412-426
-
-
AnÉ, C.1
Larget, B.2
Baum, D.A.3
Smith, S.D.4
Rokas, A.5
-
2
-
-
84555188616
-
BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics
-
AYRES, D., A. DARLING, D. ZWICKL, P. BEERLI, M. T. HOLDER, P. O. LEWIS, J. HUELSENBECK, et al. 2012. BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology 61: 170-173.
-
(2012)
Systematic Biology
, vol.61
, pp. 170-173
-
-
Ayres, D.1
Darling, A.2
Zwickl, D.3
Beerli, P.4
Holder, M.T.5
Lewis, P.O.6
Huelsenbeck, J.7
-
3
-
-
33846839295
-
Concordance trees, concordance factors, and the exploration of reticulate genealogy
-
BAUM, D. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56: 417-426.
-
(2007)
Taxon
, vol.56
, pp. 417-426
-
-
Baum, D.1
-
4
-
-
84870355484
-
-
Roberts and Co., Greenwood Village, Colorado, USA
-
BAUM, D. A., and S. D. SMITH. 2013. Tree thinking: An introduction to phylogenetic biology. Roberts and Co., Greenwood Village, Colorado, USA.
-
(2013)
Tree thinking: An Introduction to Phylogenetic Biology
-
-
Baum, D.A.1
Smith, S.D.2
-
5
-
-
78650445809
-
Recent trends in molecular phylogenetic analysis: Where to next?
-
BLAIR, C., and R. W. MURPHY. 2011. Recent trends in molecular phylogenetic analysis: Where to next? Journal of Heredity 102: 130-138.
-
(2011)
Journal of Heredity
, vol.102
, pp. 130-138
-
-
Blair, C.1
Murphy, R.W.2
-
6
-
-
84861216801
-
Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives
-
BLAIR, J. E., M. D. COFFEY, and F. N. MARTIN. 2012. Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives. PLoS ONE 7: e37003.
-
(2012)
PLoS ONE
, vol.7
-
-
Blair, J.E.1
Coffey, M.D.2
Martin, F.N.3
-
7
-
-
0343891312
-
Possible relationships between wild and cultivated carrots (Daucus carota L.) in the Netherlands
-
BRANDENBURG, W. A. 1981. Possible relationships between wild and cultivated carrots (Daucus carota L.) in the Netherlands. Die Kulturpflanze 29: 369-375.
-
(1981)
Die Kulturpflanze
, vol.29
, pp. 369-375
-
-
Brandenburg, W.A.1
-
8
-
-
84861329445
-
Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)
-
CAI, D., F. RODRÍGUEZ, Y. TENG, C. ANÉ, M. BONIERBALE, L. A. MUELLER, and D. M. SPOONER. 2012. Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC Evolutionary Biology 12: 70.
-
(2012)
BMC Evolutionary Biology
, vol.12
, pp. 70
-
-
Cai, D.1
RodrÍguez, F.2
Teng, Y.3
AnÉ, C.4
Bonierbale, M.5
Mueller, L.A.6
Spooner, D.M.7
-
9
-
-
74049108922
-
BLAST+: Architecture and applications
-
CAMACHO C., G. COULOURIS, V. AVAGYAN, N. MA, J. PAPADOPOULOS, K. BEALER, and T. L. MADDEN. 2009. BLAST+: Architecture and applications. BMC Bioinformatics 10: 421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
10
-
-
0035130163
-
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
-
CHEN, F. C., and W. H. LI. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics 68: 444-456.
-
(2001)
American Journal of Human Genetics
, vol.68
, pp. 444-456
-
-
Chen, F.C.1
Li, W.H.2
-
12
-
-
79955079429
-
A multi gene sequence-based phylogeny of the Musaceae (banana) family
-
CHRISTELOVÁ, P., M. VALÁRIK, E. H IBOVÁ, E. DE LANGHE, and J. DOLEŽEL. 2011. A multi gene sequence-based phylogeny of the Musaceae (banana) family. BMC Evolutionary Biology 11: 103.
-
(2011)
BMC Evolutionary Biology
, vol.11
, pp. 103
-
-
ChristelovÁ, P.1
ValÁrik, M.2
IbovÁ, E.H.3
Langhe, E.D.4
DoleŽel, J.5
-
13
-
-
70450231658
-
Species trees from highly incongruent gene trees in rice
-
CRANSTON, K., B. HURWITZ, D. WARE, L. STEIN, and R. A. WING. 2009. Species trees from highly incongruent gene trees in rice. Systematic Biology 58: 489-500.
-
(2009)
Systematic Biology
, vol.58
, pp. 489-500
-
-
Cranston, K.1
Hurwitz, B.2
Ware, D.3
Stein, L.4
Wing, R.A.5
-
14
-
-
84864453108
-
JModelTest 2: More models, new heuristics and parallel computing
-
DARRIBA, D., G. L. TABOADA, R. DOALLO, and D. Posada. 2012. JModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9: 772.
-
(2012)
Nature Methods
, vol.9
, pp. 772
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
15
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life. Nature Reviews
-
DELSUC, F., H. BRINKMANN, and H. PHILIPPE. 2005. Phylogenomics and the reconstruction of the tree of life. Nature Reviews. Genetics 6: 361-375.
-
(2005)
Genetics
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
17
-
-
0033759668
-
A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoc1 intron sequences: Towards a suprageneric classification of subfamily Apioideae
-
DOWNIE, S. R., D. S. Katz-Downie, and M. F. Watson. 2000. A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoc1 intron sequences: Towards a suprageneric classification of subfamily Apioideae. American Journal of Botany 87: 273-292.
-
(2000)
American Journal of Botany
, vol.87
, pp. 273-292
-
-
Downie, S.R.1
Katz-Downie, D.S.2
Watson, M.F.3
-
18
-
-
0042307371
-
Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations
-
DRESSMAN, D., H. YAN, G. TRAVERSO, K. W. KINZLER, and B. VOGELSTEIN. 2003. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proceedings of the National Academy of Sciences, USA 100: 8817-8822.
-
(2003)
Proceedings of the National Academy of Sciences, USA
, vol.100
, pp. 8817-8822
-
-
Dressman, D.1
Yan, H.2
Traverso, G.3
Kinzler, K.W.4
Vogelstein, B.5
-
19
-
-
0036021407
-
Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
-
DRUMMOND, A. J., G. K. NICHOLLS, A. G. RODRIGO, and W. SOLOMON. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320.
-
(2002)
Genetics
, vol.161
, pp. 1307-1320
-
-
Drummond, A.J.1
Nicholls, G.K.2
Rodrigo, A.G.3
Solomon, W.4
-
20
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
DRUMMOND, A. J., M. A. SUCHARD, D. XIE, and A. RAMBAUT. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
21
-
-
42149157760
-
Broad phylogenomics sampling improves resolution of the animal tree of life
-
DUNN, C. W., A. HEJNOL, D. Q. MATUS, K. PANG, W. E. BROWNE, S. A. SMITH, E. SEAVER, et al. 2008. Broad phylogenomics sampling improves resolution of the animal tree of life. Nature 452: 745-749.
-
(2008)
Nature
, vol.452
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
Pang, K.4
Browne, W.E.5
Smith, S.A.6
Seaver, E.7
-
22
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
EDGAR, R. C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
23
-
-
58249100073
-
Is a new and general theory of molecular systematic emerging?
-
EDWARDS, V. 2009. Is a new and general theory of molecular systematic emerging? Evolution 63: 1-19.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, V.1
-
24
-
-
84858611328
-
Applications of nextgeneration sequencing in plant biology
-
EGAN, A., J. SCHLUETER, and D. M. SPOONER. 2012. Applications of nextgeneration sequencing in plant biology. American Journal of Botany 99: 175-185.
-
(2012)
American Journal of Botany
, vol.99
, pp. 175-185
-
-
Egan, A.1
Schlueter, J.2
Spooner, D.M.3
-
25
-
-
0027799716
-
Exploitation of the resistance to carrot fly in the wild carrot species Daucus capillifolius
-
ELLIS, P. R., J. A. HARDMAN, T. C. CROWTHER, and P. L. SAW. 1993. Exploitation of the resistance to carrot fly in the wild carrot species Daucus capillifolius. Annals of Applied Biology 122: 79-91.
-
(1993)
Annals of Applied Biology
, vol.122
, pp. 79-91
-
-
Ellis, P.R.1
Hardman, J.A.2
Crowther, T.C.3
Saw, P.L.4
-
26
-
-
84959743928
-
Methods for computing Wagner trees
-
FARRIS, J. S. 1970. Methods for computing Wagner trees. Systematic Zoology 19: 83-92.
-
(1970)
Systematic Zoology
, vol.19
, pp. 83-92
-
-
Farris, J.S.1
-
27
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
FELSENSTEIN, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
28
-
-
84959747425
-
Toward defining the course of evolution: Minimum change for a specific tree topology
-
FITCH, W. 1971. Toward defining the course of evolution: Minimum change for a specific tree topology. Systematic Zoology 20: 406-416.
-
(1971)
Systematic Zoology
, vol.20
, pp. 406-416
-
-
Fitch, W.1
-
29
-
-
84908002963
-
-
FAOSTAT, Rome, Italy. Website, [accessed 4 March 2014]
-
FAO [FOOD AND AGRICULTURAL ORGANIZATION OF THE UNITED NATIONS]. 2012. FAOSTAT, Rome, Italy. Website http://www.faostat.fao.org [accessed 4 March 2014].
-
(2012)
-
-
-
30
-
-
0035984048
-
Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants
-
FULTON, T. M., R. VAN DER HOEVEN, N. T. EANNETTA, and S. D. TANKSLEY. 2002. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467.
-
(2002)
Plant Cell
, vol.14
, pp. 1457-1467
-
-
Fulton, T.M.1
Van Der Hoeven, R.2
Eannetta, N.T.3
Tanksley, S.D.4
-
31
-
-
48049107322
-
The conditioned reconstructed process
-
GERNHARD, T. 2008. The conditioned reconstructed process. Journal of Theoretical Biology 253: 769-778.
-
(2008)
Journal of Theoretical Biology
, vol.253
, pp. 769-778
-
-
Gernhard, T.1
-
32
-
-
84856737401
-
Daucus
-
C. Kole [ed.], Springer Verlag, Berlin, Germany
-
GRZEBELUS, D., R. BARANSKI, K. SPALIK, C. ALLENDER, and P. W. SIMON. 2011. Daucus. In C. Kole [ed.], Wild crop relatives: Genomic and breeding resources, vol. 5, Vegetables, 129-216. Springer Verlag, Berlin, Germany.
-
(2011)
Wild crop relatives: Genomic and breeding resources, vol. 5, Vegetables
, pp. 129-216
-
-
Grzebelus, D.1
Baranski, R.2
Spalik, K.3
Allender, C.4
Simon, P.W.5
-
33
-
-
0036281455
-
Frost sensitivity of hybrids between wild and cultivated carrots
-
HAUSER, T. P. 2002. Frost sensitivity of hybrids between wild and cultivated carrots. Conservation Genetics 3: 73-76.
-
(2002)
Conservation Genetics
, vol.3
, pp. 73-76
-
-
Hauser, T.P.1
-
34
-
-
0035172025
-
Hybrids between wild and cultivated carrots in Danish carrot fields
-
HAUSER, T. P., and G. K. BJØRN. 2001. Hybrids between wild and cultivated carrots in Danish carrot fields. Genetic Resources and Crop Evolution 48: 499-506.
-
(2001)
Genetic Resources and Crop Evolution
, vol.48
, pp. 499-506
-
-
Hauser, T.P.1
BjØrn, G.K.2
-
35
-
-
84907962175
-
The building of the first Apiaceae genome
-
Website
-
Iorizzo, M., D. Senalik, S. Ellison, P. Cavagnaro, S. Cheng, P. Zheng, Z. Zheng, et al. 2014. The building of the first Apiaceae genome. Plant and Animal Genome XXII, San Diego, California, USA [online abstract]. Website https://pag.confex.com/pag/xxii/webprogram/Paper11512.html.
-
(2014)
Plant and Animal Genome XXII, San Diego, California, USA [online abstract]
-
-
Iorizzo, M.1
Senalik, D.2
Ellison, S.3
Cavagnaro, P.4
Cheng, S.5
Zheng, P.6
Zheng, Z.7
-
36
-
-
84877283169
-
Genetic structure and domestication of carrot (Daucus carota subsp. sativus L.) (Apiaceae)
-
IORIZZO, M., D. SENALIK, S. ELLISON, D. GRZEBELUS, P. CAVAGNARO, C. ALLENDER, J. BRUNET, et al. 2013. Genetic structure and domestication of carrot (Daucus carota subsp. sativus L.) (Apiaceae). American Journal of Botany 100: 930-938.
-
(2013)
American Journal of Botany
, vol.100
, pp. 930-938
-
-
Iorizzo, M.1
Senalik, D.2
Ellison, S.3
Grzebelus, D.4
Cavagnaro, P.5
Allender, C.6
Brunet, J.7
-
37
-
-
79960892661
-
De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity
-
IORIZZO, M., D. A. SENALIK, D. GRZEBELUS, M. BOWMAN, P. F. CAVAGNARO, M. MATVIENKO, H. ASHRAFI, et al. 2011. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics 12: 389.
-
(2011)
BMC Genomics
, vol.12
, pp. 389
-
-
Iorizzo, M.1
Senalik, D.A.2
Grzebelus, D.3
Bowman, M.4
Cavagnaro, P.F.5
Matvienko, M.6
Ashrafi, H.7
-
38
-
-
46249111315
-
Major cytogenetic landmarks and karyotype analysis in Daucus carota and other Apiaceae
-
IOVENE, M., E. GRZEBELUS, D. CARPUTO, J. JIANG, and P. W. SIMON. 2008. Major cytogenetic landmarks and karyotype analysis in Daucus carota and other Apiaceae. American Journal of Botany 95: 793-804.
-
(2008)
American Journal of Botany
, vol.95
, pp. 793-804
-
-
Iovene, M.1
Grzebelus, E.2
Carputo, D.3
Jiang, J.4
Simon, P.W.5
-
39
-
-
84873751778
-
An invariant form for the prior probability in estimation problems. Proceedings of the Royal Society of London, A
-
JEFFREYS, H. 1946. An invariant form for the prior probability in estimation problems. Proceedings of the Royal Society of London, A, Mathematical and Physical Sciences 186: 453-461.
-
(1946)
Mathematical and Physical Sciences
, vol.186
, pp. 453-461
-
-
Jeffreys, H.1
-
40
-
-
7244221755
-
Performance of maximum parsimony and maximum likelihood phylogenetics when evolution is heterogeneous
-
KOLACZKOWSKI, B., and J. W. THORNTON. 2004. Performance of maximum parsimony and maximum likelihood phylogenetics when evolution is heterogeneous. Nature 431: 980-984.
-
(2004)
Nature
, vol.431
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
41
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
KOONIN, E. V. 2005. Orthologs, paralogs, and evolutionary genomics. Annual Review of Genetics 39: 309-338.
-
(2005)
Annual Review of Genetics
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
42
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
KOREN, S., M. C. SCHATZ, B. P. WALENZ, J. MARTIN, J. T. HOWARD, G. GANAPATHY, Z. WANG, et al. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology 30: 693-700.
-
(2012)
Nature Biotechnology
, vol.30
, pp. 693-700
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
Ganapathy, G.6
Wang, Z.7
-
43
-
-
84894716572
-
Karotten: Zur Frage der Verkreuzung mit der wilden Karotte
-
KRICKL, M. 1961. Karotten: zur Frage der Verkreuzung mit der wilden Karotte. Saatgut-Wirtschaft 13: 135-136.
-
(1961)
Saatgut-Wirtschaft
, vol.13
, pp. 135-136
-
-
Krickl, M.1
-
44
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
KURTZ, S., A. PHILLIPPY, A. L. DELCHER, M. SMOOT, M. SHUMWAY, C. ANTONESCU, and S. L. SALZBERG. 2004. Versatile and open software for comparing large genomes. Genome Biology 5: R12.
-
(2004)
Genome Biology
, vol.5
, pp. R12
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
45
-
-
84876732832
-
Phylogeny of bacterial and archaeal genomes using conserved genes: Supertrees and supermatrices
-
LANG, J. M., A. E. DARLING, and J. A. EISEN. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: Supertrees and supermatrices. PLoS ONE 8: e62510.
-
(2013)
PLoS ONE
, vol.8
-
-
Lang, J.M.1
Darling, A.E.2
Eisen, J.A.3
-
46
-
-
78149256307
-
BUCKy: Gene tree/species tree reconciliation with the Bayesian concordance analysis
-
LARGET, B., S. K. KOTHA, C. N. DEWEY, and C. ANÉ. 2010. BUCKy: Gene tree/species tree reconciliation with the Bayesian concordance analysis. Bioinformatics 26: 2910-2911.
-
(2010)
Bioinformatics
, vol.26
, pp. 2910-2911
-
-
Larget, B.1
Kotha, S.K.2
Dewey, C.N.3
AnÉ, C.4
-
47
-
-
70649110122
-
Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus)
-
LEACHÉ, A. D. 2009. Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Systematic Biology 58: 547-559.
-
(2009)
Systematic Biology
, vol.58
, pp. 547-559
-
-
LeachÉ, A.D.1
-
48
-
-
0034045269
-
Phylogenetic analysis of cpDNA restriction sites and rpsl6 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae and related taxa
-
LEE, B. Y., and S. R. DOWNIE. 2000. Phylogenetic analysis of cpDNA restriction sites and rpsl6 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae and related taxa. Plant Systematics and Evolution 221: 35-60.
-
(2000)
Plant Systematics and Evolution
, vol.221
, pp. 35-60
-
-
Lee, B.Y.1
Downie, S.R.2
-
49
-
-
0034799705
-
Relationships within the spiny-fruited umbellifers (Scandiceae subtribes Daucinae and Torilidinae) as assessed by phylogenetic analysis of morphological characters
-
LEE, B. Y., G. A. LEVIN, and S. R. DOWNIE. 2001. Relationships within the spiny-fruited umbellifers (Scandiceae subtribes Daucinae and Torilidinae) as assessed by phylogenetic analysis of morphological characters. Systematic Botany 26: 622-642.
-
(2001)
Systematic Botany
, vol.26
, pp. 622-642
-
-
Lee, B.Y.1
Levin, G.A.2
Downie, S.R.3
-
50
-
-
73949149357
-
The utility of nuclear conserved ortholog set II (COSII) genomic regions for specieslevel phylogenetic inference in Lycium (Solanaceae)
-
LEVIN, R. A., A. WHELAN, and J. S. MILLER. 2009. The utility of nuclear conserved ortholog set II (COSII) genomic regions for specieslevel phylogenetic inference in Lycium (Solanaceae). Molecular Phylogenetics and Evolution 53: 881-890.
-
(2009)
Molecular Phylogenetics and Evolution
, vol.53
, pp. 881-890
-
-
Levin, R.A.1
Whelan, A.2
Miller, J.S.3
-
52
-
-
52949127350
-
Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species
-
LI, M., J. WUNDER, G. BISSOLI, E. SCARPONI, S. GAZZANI, E. BARBARO, H. SAEDLER, and C. VAROTTO. 2008. Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species. Cladistics 24: 727-745.
-
(2008)
Cladistics
, vol.24
, pp. 727-745
-
-
Li, M.1
Wunder, J.2
Bissoli, G.3
Scarponi, E.4
Gazzani, S.5
Barbaro, E.6
Saedler, H.7
Varotto, C.8
-
53
-
-
4644349606
-
-
Sinauer, Sunderland, Massachusetts, USA
-
MADDISON, D. R., and W. P. MADDISON. 2005. MacClade 4.08a: Analysis of phylogeny and character evolution. Sinauer, Sunderland, Massachusetts, USA.
-
(2005)
MacClade 4.08a: Analysis of phylogeny and character evolution
-
-
Maddison, D.R.1
Maddison, W.P.2
-
54
-
-
33644606488
-
Inferring phylogeny despite incomplete lineage sorting
-
MADDISON, W. P., and L. L. KNOWLES. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55: 21-30.
-
(2006)
Systematic Biology
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
55
-
-
24044455869
-
Genome sequencing in microfabricated highdensity picolitre reactors
-
MARGULIES, M., M. EGHOLM, W. ALTMAN, S. ATTIYA, J. BADER, L. BEMBEN, J. BERKA, et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437: 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.3
Attiya, S.4
Bader, J.5
Bemben, L.6
Berka, J.7
-
56
-
-
0003153330
-
Interspecific hybrid Daucus carota × D. capillifolius
-
MCCOLLUM, G. D. 1975. Interspecific hybrid Daucus carota × D. capillifolius. Botanical Gazette (Chicago, Ill.) 136: 201-206.
-
(1975)
Botanical Gazette (Chicago, Ill.)
, vol.136
, pp. 201-206
-
-
McCollum, G.D.1
-
57
-
-
0003216215
-
Hybrids of Daucus gingidium with cultivated carrots (D. carota subsp. sativus) and D. capillifolius
-
MCCOLLUM, G. D. 1977. Hybrids of Daucus gingidium with cultivated carrots (D. carota subsp. sativus) and D. capillifolius. Botanical Gazette 138: 56-63.
-
(1977)
Botanical Gazette
, vol.138
, pp. 56-63
-
-
McCollum, G.D.1
-
58
-
-
84873084821
-
Applications of next-generation sequencing to phylogeography and phylogenetics
-
MCCORMACK, J. E., S. HIRD, A. ZELLMER, B. CARSTENS, and R. BRUMFIELD. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution 66: 526-538.
-
(2013)
Molecular Phylogenetics and Evolution
, vol.66
, pp. 526-538
-
-
McCormack, J.E.1
Hird, S.2
Zellmer, A.3
Carstens, B.4
Brumfield, R.5
-
59
-
-
78751558547
-
Creating the CIPRES Science Gateway for inference of large phylogenetic trees
-
USA
-
MILLER, M. A., W. PFEIFFER, and T. SCHWARTZ. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE) in New Orleans, 2010, 1-8, USA.
-
(2010)
Proceedings of the Gateway Computing Environments Workshop (GCE) in New Orleans, 2010
, pp. 1-8
-
-
Miller, M.A.1
Pfeiffer, W.2
Schwartz, T.3
-
60
-
-
25844516325
-
Phylogenetic MCMC algorithms are misleading on mixtures of trees
-
MOSSEL, E., and E. VIGODA. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309: 2207-2209.
-
(2005)
Science
, vol.309
, pp. 2207-2209
-
-
Mossel, E.1
Vigoda, E.2
-
61
-
-
0034053509
-
Male sterility in populations of Daucus and the development of alloplasmic male-sterile lines of carrot
-
NOTHNAGEL, T., P. STRAKA, and B. LINKE. 2000. Male sterility in populations of Daucus and the development of alloplasmic male-sterile lines of carrot. Plant Breeding 119: 145-152.
-
(2000)
Plant Breeding
, vol.119
, pp. 145-152
-
-
Nothnagel, T.1
Straka, P.2
Linke, B.3
-
62
-
-
48449105928
-
IDT SciTools: A suite for analysis and design of nucleic acid oligomers
-
OWCZARZY, R., A. V. TATAUROV, Y. WU, J. A. MANTHEY, K. A. MCQUISTEN, H. G. ALMABRAZI, K. F. PEDERSEN, et al. 2008. IDT SciTools: A suite for analysis and design of nucleic acid oligomers. Nucleic Acids Research 36: W163-W169.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. W163-W169
-
-
Owczarzy, R.1
Tataurov, A.V.2
Wu, Y.3
Manthey, J.A.4
McQuisten, K.A.5
Almabrazi, H.G.6
Pedersen, K.F.7
-
64
-
-
0031110886
-
From gene to organismal phylogeny: Reconciled trees and the gene tree species tree problem
-
PAGE, R. D. M., and M. A. CHARLESTON. 1997. From gene to organismal phylogeny: Reconciled trees and the gene tree species tree problem. Molecular Phylogenetics and Evolution 7: 231-240.
-
(1997)
Molecular Phylogenetics and Evolution
, vol.7
, pp. 231-240
-
-
Page, R.D.M.1
Charleston, M.A.2
-
65
-
-
0023822631
-
Relationships between gene trees and species trees
-
PAMILO, P., and M. NEI. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5: 568-583.
-
(1988)
Molecular Biology and Evolution
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Nei, M.2
-
66
-
-
79953716259
-
Resolving difficult phylogenetic questions: Why more sequences are not enough
-
PHILIPPE, H., H. BRINKMANN, D. V. LAVROV, D. T. J. LITTLEWOOD, M. MANUEL, G. WORHEIDE, and D. BAURAIN. 2011. Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biology 9: e1000602.
-
(2011)
PLoS Biology
, vol.9
-
-
Philippe, H.1
Brinkmann, H.2
Lavrov, D.V.3
Littlewood, D.T.J.4
Manuel, M.5
Worheide, G.6
Baurain, D.7
-
67
-
-
4143122089
-
Phylogenomics of eukaryotes: Impact of missing data on large alignments
-
PHILIPPE, H., E. A. SNELL, E. BAPTESTE, P. LOPEZ, P. W. H. HOLLAND, and D. CASANE. 2004. Phylogenomics of eukaryotes: Impact of missing data on large alignments. Molecular Biology and Evolution 21: 1740-1752.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 1740-1752
-
-
Philippe, H.1
Snell, E.A.2
Bapteste, E.3
Lopez, P.4
Holland, P.W.H.5
Casane, D.6
-
69
-
-
0000370339
-
Evolutionary patterns in Apiaceae: Inferences based on matK sequence data
-
PLUNKETT, G. M., D. E. SOLTIS, and P. S. SOLTIS. 1996. Evolutionary patterns in Apiaceae: Inferences based on matK sequence data. Systematic Botany 21: 477-495.
-
(1996)
Systematic Botany
, vol.21
, pp. 477-495
-
-
Plunkett, G.M.1
Soltis, D.E.2
Soltis, P.S.3
-
70
-
-
0033952185
-
Hybridization, introgression, and linkage evolution
-
RIESEBERG, L. H., S. J. BAIRD, and K. A. GARDNER. 2000. Hybridization, introgression, and linkage evolution. Plant Molecular Biology 42: 205-224.
-
(2000)
Plant Molecular Biology
, vol.42
, pp. 205-224
-
-
Rieseberg, L.H.1
Baird, S.J.2
Gardner, K.A.3
-
71
-
-
84907962173
-
-
ROCHE, Website, [accessed 18 July 2014]
-
ROCHE. 2009. Em-PCR method manual-Lib-A SV. Website http://www.high-throughput-sequencing.com/manuals_roche/emPCR_liba_sv_Oct2009.pdf [accessed 18 July 2014].
-
(2009)
Em-PCR method manual-Lib-A SV
-
-
-
72
-
-
84871779771
-
-
ROCHE, Website, [accessed 18 July 2014]
-
ROCHE. 2010. Rapid library preparation method manual. Website http://dna.uga.edu/wp-content/uploads/2013/12/GS-FLX-Titanium-RapidLibrary-RL-Preparation-Method-Manual-Roche.pdf [accessed 18 July 2014].
-
(2010)
Rapid library preparation method manual
-
-
-
73
-
-
69549118850
-
Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?
-
RODRÍGUEZ, F., F. WU, C. ANÉ, S. TANKSLEY, and D. M. SPOONER. 2009. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evolutionary Biology 9: 191.
-
(2009)
BMC Evolutionary Biology
, vol.9
, pp. 191
-
-
RodrÍguez, F.1
Wu, F.2
AnÉ, C.3
Tanksley, S.4
Spooner, D.M.5
-
74
-
-
17744398025
-
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
-
ROKAS, A., and S. B. CARROLL. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Molecular Biology and Evolution 22: 1337-1344.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 1337-1344
-
-
Rokas, A.1
Carroll, S.B.2
-
75
-
-
33751039720
-
Bushes in the tree of life
-
ROKAS, A., and S. B. CARROLL. 2006. Bushes in the tree of life. PLoS Biology 4: e352.
-
(2006)
PLoS Biology
, vol.4
, pp. e352
-
-
Rokas, A.1
Carroll, S.B.2
-
76
-
-
29344441657
-
Animal evolution and the molecular signature of radiations compressed in time
-
ROKAS, A., D. KRUGER, and S. CARROLL. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310: 1933-1938.
-
(2005)
Science
, vol.310
, pp. 1933-1938
-
-
Rokas, A.1
Kruger, D.2
Carroll, S.3
-
77
-
-
0242365676
-
Genomescale approaches to resolving incongruence in molecular phylogenies
-
ROKAS, A., B. L. WILLIAMS, N. KING, and S. B. CARROLL. 2003. Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
78
-
-
84860109324
-
MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space
-
RONQUIST, F., M. TESLENKO, P. VAN DER MARK, D. L. AYRES, A. DARLING, S. HÖHNA, B. LARGET, et al. 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
-
(2012)
Systematic Biology
, vol.61
, pp. 539-542
-
-
Ronquist, F.1
Teslenko, M.2
Van Der Mark, P.3
Ayres, D.L.4
Darling, A.5
HÖhna, S.6
Larget, B.7
-
79
-
-
53649100100
-
The development and impact of 454 sequencing
-
ROTHBERG, J. M., and J. H. LEAMON. 2008. The development and impact of 454 sequencing. Nature Biotechnology 26: 1117-1124.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1117-1124
-
-
Rothberg, J.M.1
Leamon, J.H.2
-
80
-
-
0003875221
-
-
CABI, New York, New York, USA
-
RUBATZKY, V. E., C. F. QUIROS, and P. W. SIMON. 1999. Carrots and related vegetable Umbelliferae. CABI, New York, New York, USA.
-
(1999)
Carrots and related vegetable Umbelliferae
-
-
Rubatzky, V.E.1
Quiros, C.F.2
Simon, P.W.3
-
83
-
-
84878113118
-
Inferring ancient divergences requires genes with strong phylogenetic signals
-
SALICHOS, L., and A. ROKAS. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-333.
-
(2013)
Nature
, vol.497
, pp. 327-333
-
-
Salichos, L.1
Rokas, A.2
-
84
-
-
0017681196
-
DNA sequencing with chain-terminating inhibitors
-
SANGER, F., S. NICKLEN, and A. R. COULSON. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, USA 74: 5463-5467.
-
(1977)
Proceedings of the National Academy of Sciences, USA
, vol.74
, pp. 5463-5467
-
-
Sanger, F.1
Nicklen, S.2
Coulson, A.R.3
-
85
-
-
58849142045
-
Concatenated analysis sheds light on early metazoan evolution and fuels a modern ‘‘urmetazoon’’ hypothesis
-
SCHIERWATER, B., M. EITEL, W. JAKOB, H. J. OSIGUS, H. HADRYS, S. L. DELLAPORTA, S. O. KOLOKOTRONIS, and R. DESALLE. 2009. Concatenated analysis sheds light on early metazoan evolution and fuels a modern ‘‘urmetazoon’’ hypothesis. PLoS Biology 7: e1000020.
-
(2009)
PLoS Biology
, vol.7
-
-
Schierwater, B.1
Eitel, M.2
Jakob, W.3
Osigus, H.J.4
Hadrys, H.5
Dellaporta, S.L.6
Kolokotronis, S.O.7
Desalle, R.8
-
86
-
-
53649106195
-
Next-generation DNA sequencing
-
SHENDURE, J., and H. JI. 2008. Next-generation DNA sequencing. Nature Biotechnology 26: 1135-1145.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
87
-
-
61349143975
-
Plant breeding for human nutrition
-
SIMON, P., L. POLLAK, B. CLEVIDENCE, J. HOLDEN, and D. HAYTOWITZ. 2009. Plant breeding for human nutrition. Plant Breeding Reviews 31: 325-392.
-
(2009)
Plant Breeding Reviews
, vol.31
, pp. 325-392
-
-
Simon, P.1
Pollak, L.2
Clevidence, B.3
Holden, J.4
Haytowitz, D.5
-
88
-
-
84886257984
-
The potential of genomics in plant systematics
-
SOLTIS, D. E., M. A. GITZENDANNER, G. STULL, M. CHESTER, A. CHANDERBALI, S. CHAMALA, I. Jordon-Thaden, et al. 2013. The potential of genomics in plant systematics. Taxon 62: 886-898.
-
(2013)
Taxon
, vol.62
, pp. 886-898
-
-
Soltis, D.E.1
Gitzendanner, M.A.2
Stull, G.3
Chester, M.4
Chanderbali, A.5
Chamala, S.6
Jordon-Thaden, I.7
-
89
-
-
36249005946
-
Intercontinental disjunctions in Cryptotaenia (Apiaceae, Oenantheae): An appraisal using molecular data
-
SPALIK, K., and S. R. DOWNIE. 2007. Intercontinental disjunctions in Cryptotaenia (Apiaceae, Oenantheae): An appraisal using molecular data. Journal of Biogeography 34: 2039-2054.
-
(2007)
Journal of Biogeography
, vol.34
, pp. 2039-2054
-
-
Spalik, K.1
Downie, S.R.2
-
90
-
-
77957077442
-
Amphitropic amphiantarctic disjunctions in Apiaceae subfamily Apioideae
-
SPALIK, K., M. Piwczyński, C. A. Danderson, R. Kurzyna-Młynik, T. S. Bone, and S. R. Downie. 2010. Amphitropic amphiantarctic disjunctions in Apiaceae subfamily Apioideae. Journal of Biogeography 37: 1977-1994.
-
(2010)
Journal of Biogeography
, vol.37
, pp. 1977-1994
-
-
Spalik, K.1
Piwczyński, M.2
Danderson, C.A.3
Kurzyna-Młynik, R.4
Bone, T.S.5
Downie, S.R.6
-
91
-
-
84885629131
-
Molecular phylogeny of Daucus
-
SPOONER, D. M., P. ROJAS, M. BONIERBALE, L. A. MUELLER, M. SRIVASTAV, D. SENALIK, and P. SIMON. 2013. Molecular phylogeny of Daucus. Systematic Botany 38: 850-857.
-
(2013)
Systematic Botany
, vol.38
, pp. 850-857
-
-
Spooner, D.M.1
Rojas, P.2
Bonierbale, M.3
Mueller, L.A.4
Srivastav, M.5
Senalik, D.6
Simon, P.7
-
92
-
-
84894864238
-
Reassessment of practical subspecies identifications of the USDA Daucus carota germplasm collection: Morphological data
-
SPOONER, D. M., M. P. WIDRLECHNER, K. R. REITSMA, D. E. PALMQUIST, S. ROUZ, Z. Ghrabi-Gammar, M. Neffati, et al. 2014. Reassessment of practical subspecies identifications of the USDA Daucus carota germplasm collection: Morphological data. Crop Science 54: 706-718.
-
(2014)
Crop Science
, vol.54
, pp. 706-718
-
-
Spooner, D.M.1
Widrlechner, M.P.2
Reitsma, K.R.3
Palmquist, D.E.4
Rouz, S.5
Ghrabi-Gammar, Z.6
Neffati, M.7
-
93
-
-
0001487303
-
An isozyme-based assessment of the genetic variability within the Daucus carota complex (Apiaceae: Caucalideae)
-
ST. Pierre, M. D., R. J. Bayer, and I. M. Weiss. 1990. An isozyme-based assessment of the genetic variability within the Daucus carota complex (Apiaceae: Caucalideae). Canadian Journal of Botany 68: 2449-2457.
-
(1990)
Canadian Journal of Botany
, vol.68
, pp. 2449-2457
-
-
Pierre, S.T.1
Bayer, R.J.2
Weiss, I.M.3
-
94
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
STAMATAKIS, A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
95
-
-
0001547111
-
Inheritance of chloroplast and mitochondrial DNA in alloplasmic forms of the genus Daucus
-
STEINBORN, R., B. LINKE, T. NOTHNAGEL, and T. BÖRNER. 1995. Inheritance of chloroplast and mitochondrial DNA in alloplasmic forms of the genus Daucus. Theoretical and Applied Genetics 91: 632-638.
-
(1995)
Theoretical and Applied Genetics
, vol.91
, pp. 632-638
-
-
Steinborn, R.1
Linke, B.2
Nothnagel, T.3
BÖrner, T.4
-
97
-
-
0024713112
-
Gene genealogy in three related populations: Consistency probability between gene and population trees
-
TAKAHATA, N. 1989. Gene genealogy in three related populations: Consistency probability between gene and population trees. Genetics 122: 957-966.
-
(1989)
Genetics
, vol.122
, pp. 957-966
-
-
Takahata, N.1
-
98
-
-
84894730763
-
Pollination of the cultivated carrot (Daucus carota L.) by the wild carrot (D. carota var. maximus), and its implications on commercial seed production
-
[In Hebrew, English summary]
-
UMIEL, N., R. JACOBSON, and D. GLOBERSON. 1975. Pollination of the cultivated carrot (Daucus carota L.) by the wild carrot (D. carota var. maximus), and its implications on commercial seed production. Hassadeh 56: 478-480 [In Hebrew, English summary].
-
(1975)
Hassadeh
, vol.56
, pp. 478-480
-
-
Umiel, N.1
Jacobson, R.2
Globerson, D.3
-
99
-
-
77953541727
-
-
USDA [U. S. DEPARTMENT OF AGRICULTURE], NATIONAL AGRICULTURAL STATISTICS SERVICE, Website, [accessed 4 March 2014]
-
USDA [U. S. DEPARTMENT OF AGRICULTURE], NATIONAL AGRICULTURAL STATISTICS SERVICE. 2012. Data and statistics. Website http://www.nass.usda.gov/Data_and_Statistics/index.asp [accessed 4 March 2014].
-
(2012)
Data and statistics
-
-
-
100
-
-
0032970668
-
Phylogeny and relationships in Daucus based on restriction fragment length polymorphisms (RFLPs) of the chloroplast and mitochondrial genomes
-
VIVEK, B. S., and P. SIMON. 1999. Phylogeny and relationships in Daucus based on restriction fragment length polymorphisms (RFLPs) of the chloroplast and mitochondrial genomes. Euphytica 105: 183-189.
-
(1999)
Euphytica
, vol.105
, pp. 183-189
-
-
Vivek, B.S.1
Simon, P.2
-
101
-
-
0000162362
-
Phylogenetic incongruence: Window into genome history and molecular evolution
-
D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Kluwer, Boston, Massachusetts, USA
-
WENDEL, J. F., and J. J. DOYLE. 1998. Phylogenetic incongruence: Window into genome history and molecular evolution. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II: DNA sequencing, 265-296. Kluwer, Boston, Massachusetts, USA.
-
(1998)
Molecular systematics of plants II: DNA sequencing
, pp. 265-296
-
-
Wendel, J.F.1
Doyle, J.J.2
-
102
-
-
0000089703
-
Interactions between wild and cultivated carrots (Daucus carota L.)
-
WIJNHEIJMER, E. H. M., W. A. BRANDENBURG, and S. J. TER BORG. 1989. Interactions between wild and cultivated carrots (Daucus carota L.). Euphytica 40: 147-154.
-
(1989)
Euphytica
, vol.40
, pp. 147-154
-
-
Wijnheijmer, E.H.M.1
Brandenburg, W.A.2
Borg, S.J.T.3
-
103
-
-
84879418928
-
Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
-
WILLIAMS, J. S., J. H. NIEDZWIECKI, and D. W. WEISROCK. 2013. Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Molecular Phylogenetics and Evolution 68: 671-682.
-
(2013)
Molecular Phylogenetics and Evolution
, vol.68
, pp. 671-682
-
-
Williams, J.S.1
Niedzwiecki, J.H.2
Weisrock, D.W.3
-
104
-
-
33751344142
-
Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the euasterid plant clade
-
WU, F., L. A. MUELLER, D. CROUZILLAT, V. PÉTIARD, and S. D. TANKSLEY. 2006. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the euasterid plant clade. Genetics 174: 1407-1420.
-
(2006)
Genetics
, vol.174
, pp. 1407-1420
-
-
Wu, F.1
Mueller, L.A.2
Crouzillat, D.3
PÉtiard, V.4
Tanksley, S.D.5
-
105
-
-
33750387249
-
-
Ph.D. dissertation, University of Texas at Austin, Austin, Texas, USA
-
ZWICKL, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, University of Texas at Austin, Austin, Texas, USA.
-
(2006)
Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion
-
-
Zwickl, D.J.1
|