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The interaction between the nuclear and chloroplast genomes in plants is crucial for preserving essential cellular functions in the face of varying rates of mutation, levels of selection, and modes of transmission. Despite this, identifying nuclear genes that coevolve with chloroplast genomes at a genome-wide level has remained a challenge. In this study, we conducted an evolutionary rate covariation analysis to identify candidate nuclear genes coevolving with chloroplast genomes in Juglandaceae. Our analysis was based on 4,894 orthologous nuclear genes and 76 genes across seven chloroplast partitions in nine Juglandaceae species. Our results indicated that 1,369 (27.97%) of the nuclear genes demonstrated signatures of coevolution, with the Ycf1/2 partition yielding the largest number of hits (765) and the ClpP1 partition yielding the fewest (13). These hits were found to be significantly enriched in biological processes related to leaf development, photoperiodism, and response to abiotic stress. Among the seven partitions, AccD, ClpP1, MatK, and RNA polymerase partitions and their respective hits exhibited a narrow range, characterized by d N /d S values below 1. In contrast, the Ribosomal, Photosynthesis, Ycf1/2 partitions and their corresponding hits, displayed a broader range of d N /d S values, with certain values exceeding 1. Our findings highlight the differences in the number of candidate nuclear genes coevolving with the seven chloroplast partitions in Juglandaceae species and the correlation between the evolution rates of these genes and their corresponding chloroplast partitions. [ABSTRACT FROM AUTHOR]

Summary: Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance.We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance.Our findings indicate that the chloroplast genome had substantially deeper divergence (branch‐length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation‐by‐distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome.Altogether, this study highlights a critical role of sex‐biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance. [ABSTRACT FROM AUTHOR]

Aim Investigating phytogeographical divides can help provide a better understanding of the evolution of floras. Tertiary relict floras in East Asia have been subdivided into a northern region ( NEA) and a southern region ( SEA), separated by an arid belt, although this division remains little-studied since it was proposed in 2002. To test its validity, we investigated the evolutionary history of a Tertiary relict species, Lindera obtusiloba. Location East Asia. Methods Chloroplast DNA (cp DNA) and nuclear microsatellites ( nSSRs) were genotyped in 34 populations. Regional genetic diversities were compared, and genetic differentiation was calculated between and within regions. Bayesian phylogenetics and Bayesian clustering were employed for phylogeographic reconstruction. The time to the most recent common ancestor ( TMRCA) and divergence time between the two regions were estimated. Historical rates of gene flow were calculated using the maximum-likelihood method. The potential habitat at present, during the Last Glacial Maximum ( LGM) and during the Last Interglacial ( LIG) were predicted by ecological niche modelling ( ENM). Results Both markers revealed sharp genetic discontinuities and limited migration between regions. The TMRCA and population divergence can probably both be dated to the Pliocene. Clear genetic structure was found within each region. The genetic diversity of both markers and the age of chlorotypes decreased with increasing longitude within SEA. Japan harboured the highest genetic diversity within NEA, with abundant private and ancestral chlorotypes. NEA had greater genetic diversity than SEA in nSSRs, whereas the opposite was true for cp DNA. ENM in LGM and LIG may support long-term isolation in multiple locations in both regions. Main conclusions Our study provides solid evidence for the proposed floral subdivision along the arid belt within East Asia. Populations in both regions remained stable over a long period and sustained multiple glacial refugia. Westernmost SEA and easternmost NEA sustained ancestral populations. Clear eastward expansion was detected within SEA. [ABSTRACT FROM AUTHOR]

East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach., We genotyped 70 populations throughout the distributional range of Asian butternuts ( Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single-copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades., The genetic data consistently identified two clades, one northern, comprising Juglans mandshurica and Juglans ailantifolia, and one southern, comprising Juglans cathayensis. The two clades diverged through climate-induced vicariance of an ancestral northern range during the mid-Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north-south divergence., Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene. [ABSTRACT FROM AUTHOR]