Index Herbariorum

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1. Little DP (2006) Evolution and circumscription of the true cypresses (Cupressaceae: Cupressus). Syst Bot 31:461-480.

2. Little DP, Schwarzbach AE, Adams RP, Hsieh CF (2004) The circumscription and phylogenetic relateonships of Callitropsis and the newly described genus Xanthocyparis (Cupressaceae). Am J Bot 91:1872-1881.

3. Kusumi J, Tsumura Y, Yoshimaru H, Tachida H (2000) Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences. Am J Bot 87:1480-1488.

4. Sinclair WT, et al. (2002) Evolutionary relationships of the New Caledonian heterotrophic conifer, Parasitaxus usta (Podocarpaceae), inferred from chloroplast trnL-F intron/spacer and nuclear rDNA ITS2 sequences. Plant Syst Evol 233:79-104.

5. Setoguchi H, Osawa TA, Pintaud JC, Jaffre T, Veillon JM (1998) Phylogenetic relationships within Araucariaceae based on rbcL gene sequences. Am J Bot 85:1507-1516.

6. Liu N, et al. (2009) Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes. Chinese Sci Bull 54:2648-2655.

7. Conran JG, et al. (2000) Generic relationships within and between the gymnosperm families Podocarpaceae and Phyllocladaceae based on an analysis of the chloroplast gene rbcL. Aust J Bot 48:715-724.

8. Sanderson MJ, Wojciechowski MF, Hu JM, Khan TS, Brady SG (2000) Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants. Mol Biol Evol 17:782-797.

9. Quinn CJ, Price RA, Gadek PA (2002) Familial concepts and relationships in the conifers based on rbcL and matK sequence comparisons. Kew Bull 57:513-531.

10. Borsch T, et al. (2003) Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J Evol Biol 16:558-576.

11. Cheng YC, Nicolson RG, Tripp K, Chaw SM (2000) Phylogeny of Taxaceae and Cephalotaxaceae genera inferred from chloroplast matK gene and nuclear rDNA ITS region. Mol Phylogenet Evol 14:353-365.

12. Hao DC, Huang BL, Chen SL, Mu J (2009) Evolution of the chloroplast trnL-trnF region in the gymnosperm lineages Taxaceae and Cephalotaxaceae. Biochem Genet 47:351-369.

13. Wagstaff SJ (2004) Evolution and biogeography of the austral genus Phyllocladus (Podocarpaceae). J Biogeogr 31:1569-1577.

14. Rai HS, O'Brien HE, Reeves PA, Olmstead RG, Graham SW (2003) Inference of higher-order relationships in the Cycads from a large chloroplast data set. Mol Phylogenet Evol 29:350-359.

15. Wang XQ, Shu YQ (2000) Chloroplast matK gene phylogeny of Taxaceae and Cephalotaxaceae, with additional reference to the systematic position of Nageia. Acta Phytotaxon Sin 38:201-210.

16. Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84.

17. Tsumura Y, Suyama Y (1998) Differentiation of mitochondrial DNA polymophisms in populations of five Japanese Abies species. Evolution 52:1031-1042.

18. Wang XQ, Tank DC, Sang T (2000) Phylogeny and divergence times in Pinaceae: Evidence from three genomes. Mol Biol Evol 17:773-781.

19. Havill NP et al. (2008) Phylogeny and biogeography of Tsuga (Pinaceae) inferred from nuclear ribosomal ITS and chloroplast DNA sequence data. Syst Bot 33:478-489.

20. Lin CP, Huang JP, Wu CS, Hsu CY, Chaw SM (2010) Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Genome Biol Evol 2:504-517.

21. Ran JH, Wei XX, Wang XQ (2006) Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes. Mol Phylogenet Evol 41:405-419.

22. Qiao CY, Ran JH, Li Y, Wang XQ (2007) Phylogeny and biogeography of Cedrus (Pinaceae) inferred from sequences of seven paternal chloroplast and maternal mitochondrial DNA regions. Ann Bot-London 100:573-580.

23. Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM (2009) Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol 52:115-124.

24. Cronn R, et al. (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e122.

25. Leebens-Mack J, et al. (2005) Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the felsenstein zone. Mol Biol Evol 22:1948-1963.

26. Lohne C, Borsch T (2005) Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. Mol Biol Evol 22:317-332.

27. Chaw SM, Walters TW, Chang CC, Hu SH, Chen SH (2005) A phylogeny of Cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region. Mol Phylogenet Evol 37:214-234.

28. Wu CS, Wang YN, Liu SM, Chaw SM (2007) Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol 24:1366-1379.

29. Shi S, et al. (2000) Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences. Theor Appl Genet 101:925-930.

30. Cai ZQ, et al. (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of Magnoliids. BMC Evol Biol 6:77.

31. Chaw SM, Zharkikh A, Sung HM, Lau TC, Li WH (1997) Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol Biol Evol 14:56-68.

32. Bowe LM, Coat G, dePamphilis CW (2000) Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proc Natl Acad Sci USA 97:4092-4097.

33. Qiu YL, et al. (2006) The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA 103:15511-15516.

34. Kelch DG (2002) Phylogenetic assessment of the monotypic genera Sundacarpus and Manoao (Coniferales: Podocarpaceae) utilising evidence from 18S rDNA sequences. Aust Syst Bot 15:29-35.

35. Chaw SM, Sung HM, Long H, Zharkikh A, Li WH (1995) The phylogenetic positions of the conifer genera Amentotaxus, Phyllocladus and Nageia inferred from 18S rRNA sequences. J Mol Evol 41:224-230.

36. Chaw SM, Long H, Wang BS, Zharkikh A, Li WH (1993) The phylogenetic position of Taxaceae based on 18S rRNA sequences. J Mol Evol 37:624-630.

37. Kelch DG (1998) Phylogeny of the Podocarpaceae: comparison of evidence from morphology and 18s rDNA. Am J Bot 85:986-996.

38. Qiu YL, et al. (1999) The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402:404-407.

39. Qiu YL, et al. (2005) Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Int J Plant Sci 166:815-842.

40. Zanis MJ, Soltis PS, Qiu YL, Zimmer E, Soltis DE (2003) Phylogenetic analyses and perianth evolution in basal angiosperms. Ann Mo Bot Gard 90:129-150.

41. Wang D, et al. (2007) Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. Mol Biol Evol 24:2040-2048.

42. Chaw SM, et al. (2008) The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Mol Biol Evol 25:603-615.

43. Parkinson CL, Adams KL, Palmer JD (1999) Multigene analyses identify the three earliest lineages of extant flowering plants. Curr Biol 9:1485-1488.
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