Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution

Abstract

Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species‐rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction‐site‐associated DNA sequencing data. We assessed the congruence of topologies generated from different datasets and employed several approaches to reveal the causes of phylogenetic incongruence, including the detection of hybridization and introgression using PhyloNetworks and the D‐statistic test (ABBA‐BABA test). We found that, in the plastome‐based phylogeny, Fargesia bamboos can be clustered into three groups and Yushania was nested within one of them, which contradicts the nuclear–double digest restriction‐site‐associated DNA sequencing‐based phylogeny. Moreover, the genetic variation of chloroplast DNA is significantly correlated with geographical distribution. The strong signal of incomplete lineage sorting, hybridization, introgression, and cytoplasmic gene flow found among genera and species suggests that reticulate evolution is the main cause for the phylogenetic incongruence between nuclear and chloroplast datasets. Our results add evidence that genomes with different inheritance patterns can reveal distinct evolutionary histories of species and suggest that reticulate evolution is prevalent in rapidly diversifying groups.

Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

“…In mesangiospermae, conflicting topologies between the plastome and nuclear trees were widely detected due to their inconsistent genetic patterns (Leebens‐Mack et al, 2019 ; Li et al, 2019 ; Ma et al, 2021 ; Yang et al, 2020 ). Several processes could explain ambiguous and conflicting topologies, such as hybridization, polyploidization, and incomplete lineage sorting (ILS; Degnan & Rosenberg, 2009 ; Paule et al, 2020 ; Rieseberg & Soltis, 1991 ; Ye et al, 2021 ). Comparing our plastid trees with biparentally inherited nuclear gene trees (Liu et al, 2021 ), incongruences were observed in the placement of P. raimondii and P. macrura .…”

Cryptic Species Diversification of the Pedicularis siphonantha Complex (Orobanchaceae) in the Mountains of Southwest China Since the Pliocene

“…Topological incongruence between nuclear/nrITS and ptDNA phylogenies has been reported in many taxa ( Rieseberg et al, 1996 ; Buckley et al, 2006 ; Stegemann et al, 2012 ; Yi et al, 2015 ; Stull et al, 2020 ; Ye et al, 2021 ). In this study, incongruences between the nrITS and ptDNA datasets were found among species within the P. siphonantha complex and in the sister relationship between the P. siphonantha complex and P. amplituba + P. tachanensis in phylogenetic analyses, as well as the estimation of genetic distance.…”

Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China

“…Phylogeographic information of species can be used to describe potential phylogeoregions ( Lin et al., 2021 ; Ye et al., 2021 ). Taking into consideration its current geographic distribution pattern, we hypothesized that the genus Heteroplexis was originally distributed in northeastern Guangxi ( H. microcephala and H. sericophylla ) and then migrated continuously southward or southwestward to central Guangxi ( H. incana and H. impressinervia ) and southwestern Guangxi ( H. vernonioides ).…”

“…In particular, restriction site-associated DNA sequencing (RADseq), which is of low cost and does not require reference genomic information to obtain a large number of genome-wide markers, has been increasingly used in phylogeographic studies ( Baird et al., 2008 ; Brandrud et al., 2020 ; Spriggs and Fertakos, 2021 ). For example, RADseq has been used to resolve complex phylogenetic relationships and species boundaries ( Rubin et al., 2012 ; Ferrer Obiol et al., 2021 ; Ye et al., 2021 ), assess genetic diversity and structure ( Cai et al., 2020 ), and infer interspecific gene flow ( Natola et al., 2021 ) and demographic history ( Hellwig et al., 2020 ; Tao et al., 2021 ). The obtained genetic information is valuable for studying species differentiation and evolutionary history.…”