Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments

Ecological adaptive differentiation alters both the species diversity and
intraspecific genetic diversity in forests, thus affecting the stability
of forest ecosystems. Therefore, knowledge of the genetic underpinnings of
the ecological adaptive differentiation of forest species is critical for
effective species conservation. In this study, single-nucleotide
polymorphisms (SNPs) from population transcriptomes were used to
investigate the spatial distribution of genetic variation in Liriodendron
to assess whether environmental variables can explain genetic divergence.
We examined the contributions of environmental variables to population
divergence and explored the genetic underpinnings of local adaptation
using a landscape genomic approach. Niche models and statistical analyses
showed significant niche divergence between L. chinense and L. tulipifera,
suggesting that ecological adaptation may play a crucial role in driving
interspecific divergence. We detected a new fine-scale genetic structure
in L. chinense, and divergence of the six groups occurred during the late
Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed
significant associations between genetic variation and multiple
environmental variables. Environmental association analyses identified 67
environmental association loci (EALs; nonsynonymous SNPs) that underwent
interspecific or intraspecific differentiation, 28 of which were
associated with adaptive genes. These 28 candidate adaptive loci provide
substantial evidence for local adaptation in Liriodendron. Our findings
reveal ecological adaptive divergence pattern between Liriodendron species
and provide novel insight into the role of heterogeneous environments in
shaping genetic structure and driving local adaptation among populations,
informing future L. chinense conservation efforts.