Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data

Abstract

Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid‐Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.

Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

“…Chloroplast genome SSRs (cpSSRs) have several essential characteristics, such as abundance, maternal inheritance, and haploid nature. Based on these features, chloroplast genome SSRs are mainly used in population genetic variation and gene flow analyses [43][44][45] and are considered valuable markers. The significance and applicability of cpSSR markers have been reported in various other Papaveroideae species, such as using cpSSR markers to assess the population genetics of opium poppy [46].…”

Genomic divergence and demographic history of Quercus aliena populations

“…Scientists are now concentrating on the nuclear genome, and genome-wide scans for genetic differentiation are a useful method to look into the potential mechanisms causing population divergence. Due to their maternally inherited traits, chloroplast genomes exhibit a clear geographical structure [ 14 , 15 ], and are therefore useful in phylogeographical studies [ 16 – 19 ]. We may therefore conduct comprehensive investigations of the genetic diversity and divergence of Q. aliena by integrating chloroplast and nuclear genome sequences.…”

Evolutionary response of cold‐adapted chasmophytic plants to Quaternary climatic oscillations in the Mountains of Central Asia (a world hotspot of biodiversity)

“…Subsequent climate changes (alternate cooling and warming) contributed to range extension, enabling the geographical contact of previously isolated gene pools. Thus, the genetic picture of present‐day populations is often the result of complex (contemporary and ancient) processes that have impacted the evolutionary history and demography of species (He et al, 2013; Hewitt, 2000; Muellner‐Riehl, 2019; Tonzo & Ortego, 2021; Vintsek et al, 2022; Wróbel et al, 2023; Xue et al, 2021).…”