An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae)

ORCID

  • Shui-Yin Liu: https://orcid.org/0000-0002-8674-7097
  • Ying-Ying Yang: https://orcid.org/0000-0001-9661-5840
  • Qin Tian: https://orcid.org/0000-0002-7939-5329
  • Zhi-Yun Yang: https://orcid.org/0009-0000-2787-1234
  • Shu-Feng Li: https://orcid.org/0000-0002-5144-4432
  • Paul J. Valdes: https://orcid.org/0000-0002-1902-3283
  • Alex Farnsworth: https://orcid.org/0000-0001-5585-5338
  • Heather R. Kates: https://orcid.org/0000-0001-8490-2201
  • Carolina M. Siniscalchi: https://orcid.org/0000-0003-3349-5081
  • Robert P. Guralnick: https://orcid.org/0000-0001-6682-1504
  • Douglas E. Soltis: https://orcid.org/0000-0001-8638-4137
  • Pamela S. Soltis: https://orcid.org/0000-0001-9310-8659
  • Gregory W. Stull: https://orcid.org/0000-0002-2733-4823
  • Ryan A. Folk: https://orcid.org/0000-0002-5333-9273
  • Ting-Shuang Yi: https://orcid.org/0000-0001-7093-9564

MSU Affiliations

University Libraries; College of Arts and Sciences; Department of Biological Sciences

Item Type

Article

Abstract

Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early-Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization-perhaps in the form of ancient syngameons like those seen today-has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.

Publication Date

9-19-2024

Publication Title

Journal of Integrative Plant Biology

Publisher

Institute of Botany, Chinese Academy of Sciences

First Page

1119

Last Page

1141

DOI

https://doi.org/10.1111/jipb.13773

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