DOI: 10.5061/dryad.0vt4b8h8n
title: Population genetic differentiation and evolutionary history in <em>Liriodendron</em> revealed by stress related single copy genes

description: Liriodendron, once widespread during the early and middle Miocene,
 developed a disjunct distribution between East Asia and North America in
 the late Miocene due to environmental changes and land bridge ruptures.
 While centers of plant origin are vital for grasping biodiversity,
 adaptation, and evolution, the specifics of Liriodendron's origin
 centers and population dynamics remain unclear, prompting this study to
 shed light on the matter. Single copy orthologue sequences, inherited with
 low mutation rates, stable across generations, serve as ideal markers for
 studying population evolution. In this study, three stress related single
 copy genes (LtDHN2, LtDHN3, and LtTLP11) were cloned and sequenced in 29
 Liriodendron populations. The gDNA datasets of LtDHN2, LtDHN3, and LtTLP11
 contained 206, 1477, and 75 polymorphic sites, respectively, with most
 genetic differences between L. chinense and L. tulipifera, moderate
 individual differences within populations, and the least among populations
 within species. Both L. tulipifera and the eastern as well as western
 populations of L. chinense have served as ancestral populations,
 exhibiting historical gene flow among each of these populations.
 Approximately 11.4-13.3 million years (Ma) ago, divergence occurred
 between L. chinense and L. tulipifera. The ancestral populations for both
 the eastern and western subpopulations of L. chinense have been traced
 back to approximately 2.19 to 2.48 million Ma. The effective population
 size of L. chinense underwent rapid expansion during two distinct
 intervals: 0.25–1.0 Ma and 0.5–1.5 Ma. Furthermore, the population of L.
 tulipifera experienced significant growth between 0.25–0.75 Ma and 0.5–2.5
 Ma. The effective population size expansion period of Liriodendron
 coincided with the environment of Quaternary glaciations, which
 significantly impacted the distribution and diversity of temperate flora
 in East Asia and North America. Understanding the historical and current
 genetic diversity of Liriodendron species provides molecular evidence for
 their origins and offers a guideline for the conservation and utilization
 of their germplasm resources.
description: # Population genetic differentiation and evolutionary history in
 *Liriodendron* revealed by stress related single copy genes
 [https://doi.org/10.5061/dryad.0vt4b8h8n](https://doi.org/10.5061/dryad.0vt4b8h8n) ## Description of the data and file structure **File: The_identified_single_copy_genes_in_Liriodendron.txt:** The amino acid FASTA files of all gene coding sequences for *L. tulipifera* and *L. chinense* were respectively download from the Phytozome ([https://phytozome-next.jgi.doe.gov/](https://phytozome-next.jgi.doe.gov/)) and NCBI ([https://www.ncbi.nlm.nih.gov/datasets/genome/](https://www.ncbi.nlm.nih.gov/datasets/genome/)) databases. Their single copy orthologue sequences were identified and compared by OrthoFinder v2.5.5. **File: LtDHN2__LtDHN3__and_LtTLP11_genes_sequences_of \_Liriodendron_populations.zip:** Includes 3 FASTA files: LtDHN2, LtDHN3 and LtTLP11 genes sequences were cloned from 29 natural populations of two *Liriodendron* species (23 of L. chinense and 6 of *L. tulipifera*) .