Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

Jialiang Li, Yujiao Zhang, Markus Rusham, Richard I. Milne, Yi Wang, Dayu Wu, Shiyu Jia, Tongzhou Tao, Kangshan Mao

Research output: Contribution to journalArticlepeer-review

Abstract

The Eastern Asia (EA) - North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2,369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade T. standishii-T. sutchuenensis and a “disjunct clade”, where western NA species T. plicata is sister to an EA-eastern NA disjunct T. occidentalis-T. koraiensis group. Our results suggested that the observed topological discordance among the gene trees as well as the cytonuclear discordance is mainly due to incomplete lineage sorting, probably facilitated by the fast diversification of Thuja around the Early Miocene and the large effective population sizes of ancestral lineages. Furthermore, ~20% of the T. sutchuenensis nuclear genome is derived from an unknown ancestral lineage of Thuja, which might explain the close resemblance of its cone morphology to that of an ancient fossil species. Overall, our study demonstrates that single genes may not resolve interspecific relationships for disjunct taxa, and that more reliable results will come from hundreds or thousands of loci, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.
Original languageEnglish
Number of pages17
JournalCladistics
Early online date22 Sep 2021
DOIs
Publication statusE-pub ahead of print - 22 Sep 2021

Keywords

  • Thuja
  • disjunct distribution
  • eastern Asia
  • North America
  • incomplete lineage sorting
  • ghost introgression

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