Local selection and adaptation
The A. viridiflora complex was already present in Asia by 1.19
Mya is evident from the age model of Fior et al. in accordance with
molecular clock estimates of the flora of Altai (A. glandulosa ,A. sibirica , and A. viridiflora ) (Fior et al., 2013). It
is clear that present lineages must have diverged much more recently
through our demographic history simulations. The model indicates that a
very young divergence time in the A. viridiflora complex: c. 239
Kya, c. 211 Kya, and c. 168 Kya (Figure 3B). Although these ages must be
explained with caution, the most important
climate
transition occurred in the Middle Pleistocene, which might have resulted
in lineage divergence by changing the suitable habitat of species. The
role of Middle Pleistocene climate transitions in speciation processes
has long been advised, such as the Ranunculus auricomus complex
(Tomasello, Karbstein, Hodač, Paetzold, & Hörandl, 2020), Populus
rotundifolia (J. L. Li et al., 2021) and Cerapanorpa brevicornis(Gao, Hua, Xing, & Hua, 2022).
Here,
we add to these “species on the speciation way” examples in the recent
Middle Pleistocene speciation and indicate that the very high rates of
speciation associated with Aquilegia adaptive radiation might be
driven by the Middle Pleistocene climate transition. Based on our
observation, the CN lineage representing A. hebeica and the NW
lineage representing A. viridiflora , which have experienced
heterogeneous environments and different environmental variables, exert
differential selection pressure on the different lineages. We found that
83 genes related to environmental factors that may play a key role in
the continuously adaptive process (Figure 4C). Some genes associated
with the abscisic acid (ABA) signaling pathway (AIN1 (Dong et
al., 2021) and AAO4 (Seo et al., 2004)) can regulate numerous ABA
responses and may induce the abiotic stress responses for defense in
different environments.
Apart from the genetic divergence revealed by phylogenetic and
population structure analyses, clear differentiation in phenotypic
traits was also exhibited based on common garden data (Figure 1).
Divergence in corolla diameter, petal length, spur length, pistil
length, inflorescence number and leaf area was probably driven by
selection. Among these traits, floral characteristic differentiation
might act as a prezygotic isolation mechanism between the four lineages.
Additionally, we found 487 genes under positive selection and exhibiting
high divergence between lineages (Figure 4A). These genes were
significantly enriched on ABC-2 type transport family protein, a gene
family involved in a wide range of metabolism in plants and playing
import roles in seed germination, stomatal movement, lateral root
development and responses to various environmental stresses (Liu, Li, &
Liu, 2013; Matsuda et al., 2012; X. D. Zhang, Zhao, & Yang, 2018).
Among these selected genes, KNU (Bollier et al., 2018) andCKX5 (Bartrina et al., 2011) are involved in the regulation of
flower morphology and development, of which a major difference exists
between the CN and NW lineages. Similarly, GRF2 (Beltramino et
al., 2018) and PHT4;2 (Irigoyen et al., 2011) initiate fixation
in those lineages due to their relation to leaf development and
morphology. NRPD1B is related to panicle branches (L. Xu et al.,
2020), and high allelic divergence and fixation of this gene in CN
lineages may contribute to producing more inflorescence relative to NW
lineages. Moreover, several genes (e.g., PAD2 (Parisy et al.,
2007), DRB3 (Mehdi et al., 2022) and EDM2 (Eulgem et al.,
2007)) are involved in disease resistance in response to biotic
stresses. Plants can adjust growth and defense based on different
environments to survive and reproduce in the natural world, which might
contribute to lineage divergence (He, Webster, & He, 2022). Therefore,
our study illuminated that geographic isolation and local selection
drove the lineage divergence of the A. viridiflora complex and
created geographic distributions of phenotypic variations. Further work
is needed to acquire more accurate functions of genes in the whole
genome under the selective pressure and clarify potential adaptation
patterns.