4.2 Phylogenetic relationships of Notholirion
The phylogenetic analysis using both nuclear gene fragments and plastid
fragments confirmed the monophyletic nature of Notholirion , which
is consistent with previous studies(Huang et al., 2018; Kim & Kim,
2018; J. Li et al., 2022). Within the genus Notholirion , the
species N. thomsonianum was found to be a sister taxon to the
branches of N. macrophyllum and N. bulbuliferum ,
representing the earliest divergence event as supported by the BEAST
divergence time estimates. Notably, some populations showed
inconsistencies in their nuclear genetic makeup. The cpDNA tree revealed
that all populations of the three Notholirion species formed
distinct monophyletic branches. However, in the ITS tree, two
populations of N. macrophyllum (MNC and MZT) clustered together
with most populations of N. bulbuliferum , while N.
bulbuliferum exhibited a population (BDY) clustered into a single
branch with the remaining two populations of N. macrophyllum .
The phenomenon of inconsistency between nuclear gene trees and
chloroplast gene trees is very common in plant phylogenetic analyses and
is typically attributed to convergent evolution, incomplete lineage
sorting, hybridization, or gene introgression(Y. Gao, Harris, Li, &
Gao, 2020; Y. D. Gao, Harris, & He, 2015; Y. D. Gao, Harris, Zhou, &
He, 2013; Huang et al., 2018; X. Liu, Wang, Shao, Ye, & Zhang, 2016).
The selected gene fragments in this study are mostly evolutionarily
conserved and less influenced by the environment, reducing the
likelihood of convergent evolution. Therefore, the main factors
considered are incomplete lineage sorting and hybridization. And in many
studies on the phylogenetic relationships of plants in the family
Liliaceae, both incomplete lineage sorting and hybridization have been
mentioned as factors contributing to conflicts in the phylogenetic
relationships(Y. Gao et al., 2020; Y. D. Gao et al., 2015; Y. D. Gao et
al., 2013; Huang et al., 2018). Studies have shown that incomplete
lineage sorting is more likely to occur when species rapidly expand or
have large population sizes(Maddison, 1997). Due to the stochastic
nature of the coalescent process, incomplete lineage sorting can lead to
random patterns of gene trees among taxa, which may result in
inconsistencies between different gene trees(Buckley, Cordeiro,
Marshall, & Simon, 2006). Furthermore, lineage sorting in plants
generally takes hundreds of millions of years(X. Liu et al., 2016;
Pelser et al., 2010). Both N. macrophyllum and N.
bulbuliferum are relatively young species that diverged in the last few
million years, which is far from reaching the timescale of hundreds of
millions of years. Therefore, we speculate that incomplete lineage
sorting may be one of the reasons for the observed incongruence between
nuclear and chloroplast genomes in Notholirion . We know that
hybridization plays a significant role in biodiversity and speciation by
either reinforcing or disrupting reproductive barriers(Les et al.,
2015). Due to the maternal inheritance of organelle genes, gene flow
resulting from biparental hybridization is usually manifested only in
nuclear genes, leading to inconsistencies between the phylogenetic trees
constructed based on nuclear genes and organellar genes(X. Liu et al.,
2016). Hybridization is widely observed in the family Liliaceae, as
evidenced by numerous reports in wild Lilium species andITS frequent use in horticulture for plant breeding purposes(Y.
Gao et al., 2020; Y. D. Gao et al., 2015; Y. D. Gao et al., 2013;
Pelkonen, Niittyvuopio, Pirttilä, Laine, & Hohtola, 2007). Furthermore,
some researchs have suggested that hybridization may be a common
phenomenon in Liliaceae plants(Douglas et al., 2011; Muratović, Robin,
Bogunić, Šoljan, & Siljak-Yakovlev, 2010). In conclusion, we speculate
that incomplete lineage sorting and hybridization may be the primary
factors leading to the conflicting phylogenetic trees observed between
the nuclear genes and chloroplast genes in Notholirion .