Genes under the selection and driven by the environment
Despite being closely related, CN and NW differ in morphology and
ecology (Figure S10). To explore the genetic mechanism of the
differentiation, we identified 1168 outlier SNPs from the 143,318
filtered SNPs according to a 0.05 threshold for the q-value between the
CN and NW lineages based on the Bayesian method applied in BAYESCAN
(Figure 4A). The outlier SNPs were in 487 genes that were identified
under positive selection (Table S8). The FST values of
outlier SNPs were significantly higher than those of others, which
suggests that the divergence of the lineages from their ancestral
population was possibly caused by strong divergent selection. GO
enrichment analyses of positively selected genes were significantly
enriched in ABC-2 type transporter family protein (GO:0016887, p= 0.0151), and we then integrated the candidate genes with organ
development, reproductive isolation, biotic and abiotic stress
responses. Among these genes , several (e.g., PAD2 (Parisy et
al., 2007), DRB3 (Mehdi, Reza, Hassan, Shima, & Gholamreza,
2022) and EDM2 (Eulgem et al., 2007)) are involved in plant
immunity, whereas some are associated with the stress of drought (e.g.,MAPKKK21 (L. Wu, Chang, Wang, Wu, & Wang, 2021) and SCL1(Manohara Reddy et al., 2018)) and cold (e.g., CER3 (Rahman et
al., 2021) and LOS1 (Bielsa, Ávila-Alonso, Fernández i Martí,
Grimplet, & Rubio-Cabetas, 2021)). Moreover, two genes (GRF2(Beltramino et al., 2018) and PHT4;2 (Irigoyen, Karlsson,
Kuruvilla, Spetea, & Versaw, 2011)) participate in the regulation of
leaf size, and several candidate genes are associated with flowering
time (e.g., FT (Tyagi et al., 2018), FLK (Lim et al.,
2004), MYB30 (L. Zhu et al., 2020) and FY (Henderson, Liu,
Drea, Simpson, & Dean, 2005)), flower organ size(KNU (Bollier et
al., 2018) and CKX5 (Bartrina, Otto, Strnad, Werner, &
Schmülling, 2011)), flower color (MYB113 (Jiao, Zhao, Wu, Song,
& Li, 2020)) and pollen development (WLIM1 (Yang et al., 2022)
and EXO70A2 (Marković et al., 2020)). The rapid divergence of
candidate genes with reproductive function might drive prezygotic
isolation across lineages.
Additionally, the Mantel test revealed a significant effect of IBD on
the genome-wide SNPs of the A. viridiflora complex (Figure 4B).
Because
genetic divergence can result from selection driven by heterogeneous
environments via geographic distance, redundancy analysis (RDA) was then
implemented to examine the bioclimatic factors related to the 143,318
SNPs. The contribution of seven environmental variables in RDA space is
shown in Figure S11. The strongest predictor was the mean diurnal range
(Bio2), followed by isothermality (Bio3), mean temperature of the
wettest quarter (Bio8), temperature seasonality (Bio4), precipitation
seasonality (Bio15), annual mean temperatures (Bio1) and precipitation
of the driest quarter (Bio17). BAYENV2 identified 179 SNPs significantly
associated with the 7 examined environmental variables (Figure 4C). The
outlier SNPs were in 83 genes and significantly enriched in “PEBP
(phosphatidylethanolamine-binding protein) family protein” (GO:0003712,
2 genes, p = 0.034), which was previously known to be involved in
various physiological processes, such as seasonal growth (Khosa,
Bellinazzo, Kamenetsky Goldstein, Macknight, & Immink, 2021), seed
germination (B. Zhang, Li, Li, & Yu, 2020) and floral transition (Y.
Zhu, Klasfeld, & Wagner, 2021). In addition, seven genes were
adaptively differentiated under temperature and water stress, indicating
that the crosstalk between the two modules observed might be important
in the process of local adaptation (Table S9).