Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Abstract

Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

Chloroplast phylogenomics and biogeography of liquorice (Leguminosae: Glycyrrhiza)

“…The uplift yielded aridification of the Asian interior and the formation of the Loess Plateau, which may have facilitated speciation of the Eurasian Glycyrrhiza sensu Meng (3.6-2.5 [113,[117][118][119][120]). The phenomenon of recent rapid diversification driven by climatic and habitat change is well known by phytogeographers, and other examples can be seen within IRLC groups (Gueldenstaedtia and Tibetia in Xie et al, [121]; Oxytropis in Shahi Shavvon et al, [122]; Astragalus in Azani et al, [123]; Hedysarum in Nafisi et al, [124]), in papilionoid genera (Ammopiptanthus in Shi et al, [125]; Sesbania in Farruggia et al,[126]), and in angiosperm taxa (Allium and mint tribe Elsholtzieae in Li et al, [127,128], respectively; Globularia and Campylanthus in Affenzeller et al, [129]; Coptis in Xiang et al, [130]; Paris in Ji et al, [131] [13,47,49]. The ancestor of the Clade II was less likely to disperse directly from eastern Asia to South America (see map in Figure 3; but see Du et al, [132]), we suspect a migration route from eastern Asia to North America via the Bering land bridge (BLB).…”

Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

“…Studies relying solely on plastid genomes and a few nuclear genes are insufficient for exploring questions of biogeography and speciation, in large part because plastid genomes are largely uniparentally inherited (Leducq et al, 2017), therefore lacking genetic evidence of both parents. Additionally, organelle genes often exhibit phylogenetic patterns significantly different from nuclear markers (Toews and Brelsford, 2012; Ji et al, 2019; Yao et al, 2019; Wang et al, 2020). In the current literature, target enrichment is emerging as the method of choice to obtain target sequence for numerous nuclear orthologs of many taxa (Wanke et al, 2017; Buys et al, 2019; Schneider et al, 2020; Granados Mendoza et al, 2020; Wang et al, 2021).…”

“…Organelle genes often exhibit phylogenetic patterns significantly different from nuclear markers (Toews and Brelsford, 2012; Leducq et al, 2017; Ji et al, 2019; Yao et al, 2019; Wang et al, 2020). Currently, target enrichment is emerging as the method of choice to obtain target sequence for numerous nuclear orthologs of many complex taxa (Wanke et al, 2017; Buys et al, 2019; Schneider et al, 2020; Granados Mendoza et al, 2020; Wang et al, 2021).…”