Incomplete lineage sorting and local extinction shaped the complex evolutionary history of the Paleogene relict conifer genus, Chamaecyparis (Cupressaceae)

Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus

“…Ancient and recent hybridization and introgression can result in rapid introgression of maternally inherited plastomes and the concerted evolution of the nuclear genes toward the introgressive species, especially for the geographically closely related species, and finally distort the phylogenetic relationships of introgressive species. In Carya , hybridization has been well studied and introgression signatures between species were evident in previous and recent reports ( Lovell et al., 2021 ; Wang et al., 2022 ). In addition to the incomplete lineage sorting and ancient plastid capture, the obvious incongruencies within subclades of Carya between plastome- and nuclear marker-based topologies in our analysis could partially result from introgressive hybridization.…”

“… Hedrick (2013) found that introgression usually involves a small number of genes or genomic regions but may be of substantial significance. Incomplete lineage sorting largely resulted from ancestral polymorphism spanning multiple speciation events and subsequent random fixation of the polymorphisms in different lineages ( Oliver, 2013 ), and it is common in multi-locus phylogenetic datasets due to rapid diversification ( Wang et al., 2022 ). The entire plastome functions as a single linked locus, with different haplotypes retained through ancient clado-genic events like the alleles of a single nuclear locus ( Folk et al., 2017 ; Lee-Yaw et al., 2019 ).…”

“…This pattern also supports the model of “the maternal phylogenetic relationship of intra-genus outcrossing species is determined by geographical distribution, and the geographically adjacent species shares a common maternal ancestor adjacent geographical distribution sharing common maternal ancestor” like the relationships among the cultivars in C. illinoinensis ( Figure 4 ). Different varieties within the same species clustered in different phylogenetic positions may be caused by their multiple matrilineal origins, for reasons such as overlapping and/or adjacent distribution regions, the hybridizability of interspecies of Carya species, or diverse plastome structure features, or wind pollination ( Wang et al., 2022 ). These results may partially account for the phylogenetic incongruencies between species in EA or NA subclades inferred from partial or complete plastome datasets or nuclear data.…”

Recent advances on phylogenomics of gymnosperms and a new classification

“…Fourth, we recognize Arceuthos , Callitropsis , Hesperocyparis , Pectinopitys C.N. Page, Sabina , and Xanthocyparis , and accept Actinostrobus and Neocallitropsis as synonyms of Callitris , and Fokienia as synonymous with Chamaecyparis ( Rushforth, 2007 ; Page, 2019 ; Wang et al., 2022 ). Fifth, we describe six new tribes (Acmopyleae, Austrocedreae, Chamaecyparideae, Microcachrydeae, Papuacedreae, and Prumnopityeae).…”

Comprehensive study of subfamily evolution through sequences of conserved nuclear genes and whole chloroplast genomes extracted from the same raw read data

“…The observed discrepancies between structural variations, pseudogenization patterns, and phylogenetic trees could be due to several factors. One potential cause is the transfer of cpDNA among plants through hybridization 23 or the phenomenon of incomplete lineage sorting 24 .…”