Display options
Cite
Li QQ, Zhou SD, Huang DQ, et al. Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera. AoB Plants. 2016;8doi: 10.1093/aobpla/plw041.
Li, Q. Q., Zhou, S. D., Huang, D. Q., He, X. J., & Wei, X. Q. (2016). Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera. AoB PLANTS, 8. https://doi.org/10.1093/aobpla/plw041
Li, Qin-Qin, et al. "Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera." AoB PLANTS vol. 8 (2016). doi: https://doi.org/10.1093/aobpla/plw041
Li QQ, Zhou SD, Huang DQ, He XJ, Wei XQ. Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera. AoB Plants. 2016 Aug 08;8. doi: 10.1093/aobpla/plw041. Print 2016. PMID: 27339054; PMCID: PMC4976397.
Copy Download .nbib Format: NLM
Share it on

AoB Plants. 2016 Aug 08;8. doi: 10.1093/aobpla/plw041. Print 2016.

Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera.

AoB PLANTS

Qin-Qin Li, Song-Dong Zhou, De-Qing Huang, Xing-Jin He, Xian-Qin Wei

Affiliations

  1. Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China Inner Mongolia.
  2. Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan.
  3. Key Laboratory of Bio-Resources and Eco-Environment, MOE, College of Life Sciences, Sichuan University, Chengdu 610064, China Sichuan [email protected].

PMID: 27339054 PMCID: PMC4976397 DOI: 10.1093/aobpla/plw041

Abstract

A primary aim of historical biogeography is to identify the causal factors or processes that have shaped the composition and distribution of biotas over time. Another is to infer the evolution of geographic ranges of species and clades in a phylogenetic context. To this end, historical biogeography addresses important questions such as: Where were ancestors distributed? Where did lineages originate? Which processes cause geographic ranges to evolve through time? Allium subgenus Anguinum comprises approximately twelve taxa with a disjunct distribution in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Although both the systematic position and the geographical limits of Anguinum have been identified, to date no molecular systematic study has been performed utilizing a comprehensive sampling of these species. With an emphasis on the Anguinum eastern Asian geographical group, the goals of the present study were: (i) to infer species-level phylogenetic relationships within Anguinum, (ii) to assess molecular divergence and estimated the times of the major splits in Anguinum and (iii) to trace the biogeographic history of the subgenus. Four DNA sequences (ITS, matK, trnH-psbA, rps16) were used to reconstruct the phylogeny of Allium subgen. Anguinum RbcL sequences were used to estimate divergences time for Allium, and sequences of ITS were used to estimate the divergence times for Anguinum and its main lineages and to provide implications for the evolutionary history of the subgenus. Phylogenetic analyses for all Allium corroborate that Anguinum is monophyletic and indicate that Anguinum is composed of two sister groups: one with a Eurasian-American distribution, and the other restricted to eastern Asia. In the eastern Asian geographical group, incongruence between gene trees and morphology-based taxonomies was recovered as was incongruence between data from plastid and nuclear sequences. This incongruence is likely due to the combined effects of a recent radiation, incomplete lineage sorting, and hybridization/introgression. Divergence time estimates suggest that the crown group of Anguinum originated during the late Miocene (ca. 7.16 Mya) and then diverged and dispersed. Biogeographic analyses using statistical dispersal-vicariance analysis (S-DIVA) and a likelihood method support an eastern Asia origin of Anguinum It is inferred that in the late Pliocene/Early Pleistocene, with cooling climates and the uplift of the Himalayas and Hengduan Mountains, the ancestor of the eastern Asian alliance clade underwent a very recent radiation.

Published by Oxford University Press on behalf of the Annals of Botany Company.

Keywords: Allium; anguinum; divergence time; historical biogeography; hybridization/introgression; incomplete lineage sorting; phylogeny; radiation

References

  1. Mol Ecol. 1999 Mar;8(3):521-3 - PubMed
  2. Am J Bot. 2000 Jan;87(1):108-23 - PubMed
  3. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4707-11 - PubMed
  4. Nature. 2000 Jun 22;405(6789):907-13 - PubMed
  5. Mol Phylogenet Evol. 2000 Nov;17(2):209-18 - PubMed
  6. Science. 2001 Apr 27;292(5517):686-93 - PubMed
  7. Proc Biol Sci. 2001 Nov 7;268(1482):2211-20 - PubMed
  8. Evolution. 2001 Oct;55(10):1943-62 - PubMed
  9. Crit Rev Biochem Mol Biol. 2002;37(3):121-47 - PubMed
  10. Bioinformatics. 2003 Aug 12;19(12):1572-4 - PubMed
  11. Mol Phylogenet Evol. 2003 Dec;29(3):417-34 - PubMed
  12. Mol Ecol. 2004 Feb;13(2):349-70 - PubMed
  13. J Plant Res. 2004 Apr;117(2):109-20 - PubMed
  14. Philos Trans R Soc Lond B Biol Sci. 2004 Feb 29;359(1442):183-95; discussion 195 - PubMed
  15. Mol Biol Evol. 2005 Oct;22(10):1948-63 - PubMed
  16. Evolution. 2005 Nov;59(11):2299-311 - PubMed
  17. PLoS Biol. 2006 May;4(5):e88 - PubMed
  18. Trends Ecol Evol. 2004 Apr;19(4):198-207 - PubMed
  19. Mol Biol Evol. 2006 Aug;23(8):1602-12 - PubMed
  20. Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9124-9 - PubMed
  21. Ann Bot. 2006 Sep;98(3):465-72 - PubMed
  22. Mol Phylogenet Evol. 2006 Oct;41(1):99-117 - PubMed
  23. Mol Phylogenet Evol. 2007 Feb;42(2):347-61 - PubMed
  24. Trends Ecol Evol. 2007 May;22(5):258-65 - PubMed
  25. Mol Biol Evol. 2007 Aug;24(8):1596-9 - PubMed
  26. BMC Evol Biol. 2007 Nov 08;7:214 - PubMed
  27. Mol Phylogenet Evol. 2008 Jun;47(3):1157-72 - PubMed
  28. Syst Biol. 2008 Feb;57(1):4-14 - PubMed
  29. Mol Phylogenet Evol. 2009 Apr;51(1):100-10 - PubMed
  30. Science. 2008 Aug 22;321(5892):1054-8 - PubMed
  31. Mol Phylogenet Evol. 2008 Nov;49(2):424-34 - PubMed
  32. Mol Phylogenet Evol. 2008 Dec;49(3):997-1007 - PubMed
  33. Mol Phylogenet Evol. 2009 Nov;53(2):463-78 - PubMed
  34. Mol Phylogenet Evol. 2009 Dec;53(3):995-1009 - PubMed
  35. Mol Phylogenet Evol. 2010 Aug;56(2):848-50 - PubMed
  36. Mol Phylogenet Evol. 2010 Oct;57(1):364-79 - PubMed
  37. Syst Biol. 2010 Oct;59(5):504-17 - PubMed
  38. Mol Phylogenet Evol. 2010 Dec;57(3):978-91 - PubMed
  39. Ann Bot. 2010 Nov;106(5):775-90 - PubMed
  40. Ann Bot. 2010 Nov;106(5):709-33 - PubMed
  41. Mol Phylogenet Evol. 2011 Apr;59(1):225-44 - PubMed
  42. Am J Bot. 2010 May;97(5):856-73 - PubMed
  43. Am J Bot. 2009 Jan;96(1):349-65 - PubMed
  44. Am J Bot. 2008 Sep;95(9):1122-35 - PubMed
  45. Am J Bot. 2006 Sep;93(9):1343-56 - PubMed
  46. Am J Bot. 2006 Feb;93(2):288-303 - PubMed
  47. Am J Bot. 2006 Mar;93(3):470-9 - PubMed
  48. Am J Bot. 2004 Oct;91(10):1645-55 - PubMed
  49. Am J Bot. 2004 Oct;91(10):1666-82 - PubMed
  50. Am J Bot. 2001 Aug;88(8):1499-516 - PubMed
  51. Am J Bot. 2001 Sep;88(9):1695-703 - PubMed
  52. Mol Phylogenet Evol. 2015 Jun;87:46-9 - PubMed
  53. Evolution. 1995 Aug;49(4):718-726 - PubMed
  54. Annu Rev Genet. 1988;22:521-65 - PubMed
  55. J Mol Evol. 1980 Dec;16(2):111-20 - PubMed
  56. Mol Biol Evol. 1997 Jul;14(7):733-40 - PubMed
  57. Trends Biochem Sci. 1998 Oct;23(10):403-5 - PubMed

Publication Types