Genomic introgression underlies environmental adaptation in three species of Chinese wingnuts, Pterocarya

Intraspecific genetic variance and gene flow can support the adaptive evolution of species challenged by climate shifts or novel environmental conditions. Less well understood is how genome organization and gene flow interact in closely related species during evolutionary divergence and differentiation. Here we conducted genomic footprint analyses to determine how three species of <i>Pterocarya</i> (<i>P</i> <i>.</i> <i>stenoptera</i>, <i>P</i>. <i>hupehensis</i>, and <i>P</i>. <i>macroptera</i>), which are sympatric but occupy different elevational niches, adapted to the heterogeneous environment of the Qinling-Daba Mountains, China. We identified candidate genes for environmental adaptation (i.e., <i>PIEZO1</i>, <i>WRKY39</i>, <i>VDAC3</i>, <i>CBL1</i>, and <i>RAF</i>), and also identified regions of gene introgression between <i>P. hupehensis</i> and <i>P. macroptera</i> that show lower genetic load and higher genetic diversity than the rest of their genomes. The same introgressed regions are notably situated in areas of minimal genetic divergence yet they are characterized by elevated recombination rates. We also identified candidate genes within these introgressed regions related to environmental adaptation (<i>TPLC2, CYCH;1, LUH, bHLH112</i>, <i>GLX1</i>, <i>TLP-3</i>, and <i>ABC1</i>). Our findings have thus clarified the important role of gene flow in ecological adaptation and revealed genomic signatures of past introgression. Together, these findings provide a stronger theoretical basis for understanding the ecological adaptation and conservation of Quaternary relict woody plants in East Asia.