Phylogeography of Thlaspi arvense (Brassicaceae) in China Inferred from Chloroplast and Nuclear DNA Sequences and Ecological Niche Modeling

Int J Mol Sci. 2015 Jun 11;16(6):13339-55. doi: 10.3390/ijms160613339.

Abstract

Thlaspi arvense is a well-known annual farmland weed with worldwide distribution, which can be found from sea level to above 4000 m high on the Qinghai-Tibetan Plateau (QTP). In this paper, a phylogeographic history of T. arvense including 19 populations from China was inferred by using three chloroplast (cp) DNA segments (trnL-trnF, rpl32-trnL and rps16) and one nuclear (n) DNA segment (Fe-regulated transporter-like protein, ZIP). A total of 11 chloroplast haplotypes and six nuclear alleles were identified, and haplotypes unique to the QTP were recognized (C4, C5, C7 and N4). On the basis of molecular dating, haplotypes C4, C5 and C7 have separated from others around 1.58 Ma for cpDNA, which corresponds to the QTP uplift. In addition, this article suggests that the T. arvense populations in China are a mixture of diverged subpopulations as inferred by hT/vT test (hT ≤ vT, cpDNA) and positive Tajima's D values (1.87, 0.05 < p < 0.10 for cpDNA and 3.37, p < 0.01 for nDNA). Multimodality mismatch distribution curves and a relatively large shared area of suitable environmental conditions between the Last Glacial Maximum (LGM) as well as the present time recognized by MaxEnt software reject the sudden expansion population model.

Keywords: MaxEnt; Qinghai-Tibetan Plateau; admixture; molecular dating; population structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus / genetics*
  • China
  • DNA, Chloroplast / genetics*
  • DNA, Plant / genetics*
  • Ecosystem*
  • Evolution, Molecular
  • Genetic Variation / genetics
  • Models, Biological*
  • Phylogeny
  • Phylogeography
  • Sequence Analysis, DNA
  • Thlaspi / classification*
  • Thlaspi / genetics*

Substances

  • DNA, Chloroplast
  • DNA, Plant