Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Tree Genetics and Genomes

Volumn 2, Issue 3, 2006, Pages 132-139

  Lang, Ping ^a   Dane, Fenny ^a   Kubisiak, Thomas L ^b  

^a AUBURN UNIVERSITY   (United States)

^b USDA FOREST SERVICE   (United States)

Author keywords

Castanea; Fagaceae; Phylogenetics; trnT L F

Indexed keywords

CASTANEA; CASTANEA CRENATA; FAGACEAE;

EID: 33746888648     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-006-0036-2     Document Type: Article

References (40)

1. Applequist WL, Wallace RS (2002) Deletions in the plastid trnT-trnL intergenic spacer define clades within Cactaceae subfamily Cactoideae. Plant Syst Evol 231:153-162
2. Bakker FT, Culham A, Gomez-Martinez R, Carvalho J, Compton J, Dawtrey R, Gibby M (2000) Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions. Mol Biol Evol 17:1146-1155
3. Clegg MT, Zurawaki G (1992) Chloroplast DNA and the study of plant phylogeny: present status and future prospects. In: Doyle JJ (ed) Molecular systematics of plants. Chapman & Hall, New York, pp 275-294
4. Cummings M, King L, Kellogg E (1994) Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Mol Biol Evol 11:1-8
5. Dane F, Hawkins LK, Huang H (1999) Genetic variation and population structure of Castanea pumila var. ozarkensis. J Am Soc Hortic Sci 124:666-670
6. Dane F, Lang P, Huang H, Fu Y (2003) Intercontinental genetic divergence of Castanea species in eastern Asia and eastern North America. Heredity 91:314-321
7. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791
8. Fineschi S, Taurchini D, Villani F, Vendramin GG (2000) Chloroplast DNA polymorphism reveals little geographical structure in Castanea sativa mill. (Fagaceae) throughout southern European countries. Mol Ecol 9:1495-1503
9. Fukuda T, Yokoyama J, Ohashi H (2001) Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences. Mol Phylogenet Evol 19:246-258
10. Graham SW, Patrick A Reeves, Analiese CE Burns, Olmstead RG (2000) Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int J Plant Sci 161: S83-S96
11. Graves AH (1950) Relative blight resistance in species and hybrids of Castanea. Phytopathology 49:1125-1131
12. Huang H, Dane F, Norton JD (1994) Allozyme diversity in Chinese, Seguin and American chestnut (Castanea spp.). Theor Appl Genet 88:981-985
13. Huang H, Carey WA, Dane F, Norton JD (1996) Evaluation of Chinese chestnut cultivars for resistance to Cryphonectria parasitica. Plant Dis 80:45-47
14. Huang H, Dane F, Kubisiak TL (1998) Allozyme and RAPD analysis of the genetic diversity and geographic variation in wild populations of the American chestnut (Fagaceae). Am J Bot 85:1013-1021
15. Jaynes R (1975) Chestnut. In: Moore J (ed) Advances in fruit breeding. Purdue Univ. Press, West Lafayette, pp 490-503
16. Johnson GP (1988) Revision of Castanea sect. Balanocastanon (Fagaceae). J Arnold Arbor 69:25-49
17. Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Mo Bot Gard 87:482-498
18. Kelchner SA, Wendel JF (1996) Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr Genet 30:259-262
19. Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Mol Phylogenet Evol 8:385-397
20. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
21. Lang P, Huang H (1999) Genetic diversity and geographic variation in natural populations of the endemic Castanea species in China. Acta Bot Sin 41:651-657 (in Chinese)
22. Levinson G, Gutman G (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203-221
23. Manos PS, Stanford AM (2001) The historical biogeography of Fagaceae: tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere. Int J Plant Sci 162:S77-S93
24. Manos PS, Zhou ZK, Cannon CH (2001) Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. Int J Plant Sci 162:1361-1379
25. McDade LA, Moody ML (1999) Phylogenetic relationships among Acanthaceae: evidence from noncoding trnL-trnF chloroplast DNA sequences. Am J Bot 86:70-80
26. Morton BR (1995) Neighboring base composition and transversion/ transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc Natl Acad Sci USA 92:9717-9721
27. Nixon KC, Crepet WL (1989) Trigonobalanus (Fagaceae): taxonomic status and phylogenetic relationships. Am J Bot 6: 828-841
28. Olmstead R, Palmer JD (1994) Chloroplast DNA systematics: a review of methods and data analysis. Am J Bot 81:1205-1224
29. Qui Y, Chase MW, Parks CR (1995) A chloroplast DNA phylogenetic study of the eastern Asia-eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae). Am J Bot 82:1582-1588
30. Shaw J, Lickey EB, Beck JT, Farmer SB, LiuW, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92:142-166
31. Simmons MP, Ochotreana H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49:369-381
32. Small RL, Ryburn JA, Cronn RC, Seelanan T,Wendel JF (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. Am J Bot 85:1301-1315
33. Soltis DE, Kuzoff RK (1995) Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution 49:727-742
34. Stanford A (1998) The biogeography and phylogeny of Castanea, Fagus, and Juglans based on matK and ITS sequence data. UNC, Chapel Hill
35. Swofford DL (2000) PAUP. Phylogenetic Analysis Using Parsimony. Version 4. Sinauer Associates, Sunderland, Massachusetts
36. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105-1109
37. Vijverberg K, Bachmann K (1999) Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses. Mol Biol Evol 16:1329-1340
38. Villani F, Pigliucci M, Benedettelli S, Cherubini M (1991) Genetic differentiation among Turkish chestnut (Castanea sativa Mill) populations. Heredity 66:131-136
39. Wen J (1999) Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Annu Rev Ecol Syst 30:421-455
40. Zuker M, Mathews DH, Turner DH (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide in RNA biochemistry and biotechnology. NATO ASI Series, Kluwer, Boston