The phylogeographic histories of plants in East Asia are complex and shaped by both past large‐scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping‐by‐sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among‐population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are (1) the expectation that asymmetric hybridization or gene flow will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within‐species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from highly selfing Ipomoea lacunosa into mixed‐mating Ipomoea cordatotriloba in regions where they co‐occur. Because of the direction of this gene flow, we predicted that reproductive barrier strength would be more strongly affected in I. cordatotriloba than I. lacunosa. We also predicted that changes to reproductive barriers in sympatric I. cordatotriloba populations would affect compatibility with allopatric populations of that species. We tested these predictions by measuring the strength of a reproductive barrier to seed set across the species’ ranges. Consistent with our first prediction, we found that sympatric and allopatric I. lacunosa produce the same number of seeds in crosses with I. cordatotriloba, whereas crosses between sympatric I. cordatotriloba and I. lacunosa are more successful than crosses between allopatric I. cordatotriloba and I. lacunosa. This difference in compatibility appears to reflect an asymmetric decrease in the strength of the barrier to seed set in sympatric I. cordatotriloba, which could be caused by I. lacunosa alleles that have introgressed into I. cordatotriloba. We further demonstrated that changes to sympatric I. cordatotriloba have decreased its ability to produce seeds with allopatric populations of the same species, in line with our second prediction. Thus, in a manner analogous to cascade reinforcement, we suggest that introgression associated with hybridization not only influences between‐species isolation but can also contribute to isolation within a species.

1The interplay between hybridization and reproductive isolation is critical to the origin and 2 maintenance of species. Hybridization between species is known to affect reproductive barrier 3 strength. An extension of this relationship is the expectation that asymmetric hybridization and gene 4 flow will have asymmetric effects on reproductive barrier strength. We tested this hypothesis in a pair 5 of morning glory species which exhibit asymmetric gene flow in sympatry from highly selfing Ipomoea 6 lacunosa into mixed mating I. cordatotriloba. Because of the direction of hybridization, we predicted 7 that reproductive barrier strength would change to a greater extent in I. cordatotriloba than I. 8 lacunosa. We tested this prediction by measuring the strength of a barrier to seed set between these 9 species across their ranges. Consistent with our prediction, we found that sympatric I. cordatotriloba 10 was more compatible with range-wide I. lacunosa than allopatric I. cordatotriloba, whereas sympatric 11 and allopatric I. lacunosa were equally compatible with I. cordatotriloba. This difference likely reflects 12 an asymmetric decrease in reproductive barriers in sympatric I. cordatotriloba. We further 13 demonstrated that changes to sympatric I. cordatotriloba have decreased compatibility with allopatric 14 populations. Thus, in a manner analogous to cascade reinforcement, introgression associated with 15 asymmetric hybridization not only influences between-species isolation but also contributes to 16 isolation within a species. 17 18 Introduction 19 Reproductive barriers are fundamental to the evolution and maintenance of biological diversity. They 20 maintain the integrity of species by preventing the homogenizing effect of gene flow. However, 21 incomplete reproductive isolation is common, and consequently hybridization between species in 22 sympatry is frequent (Mallet 2005, Whitney et al. 2010). When hybridization occurs, it can affect the 23 reproductive barriers that separate species, which, in turn, affects the potential for future 24 hybridization between those species. Species that initially hybridize in sympatry may collapse into a 25 single species, complete speciation by undergoing reinforcement, or coexist in stable hybrid zones 26 (Abbott et al. 2013, Todesco et al. 2016). Whether reproductive isolation increases, decreases, or 27 remains unchanged during hybridization thus determines species boundaries in contact zones. 28 29Hybridization affects reproductive barrier strength in two major ways: by homogenizing genotypes 30 and traits and through interactions with natural selection. First, hybridization that results in 31 introgression can cause traits that were previously differentiated between species to converge. If 32 those traits underlie reproductive barriers, the strength of reproductive isolation between species will 33 change. For example, when a trait that causes assortative mating on its own (e.g., self-referential 34 mating preferences, selfing) spreads to a new species, reproductive...

Chrysanthemum (Chrysanthemum morifolium Ramat) is an important floricultural crop and medicinal herb. Modern chrysanthemum cultivars have complex genetic backgrounds because of multiple cycles of hybridization, polyploidization, and prolonged cultivation. Understanding the genetic background and hybrid origin of modern chrysanthemum cultivars can provide pivotal information for chrysanthemum genetic improvement and breeding. By now, the origin of cultivated chrysanthemums remains unclear. In this study, 36 common chrysanthemum cultivars from across the world and multiple wild relatives were studied to identify the maternal donor of modern chrysanthemum. Chloroplast (cp) genomes of chrysanthemum cultivars were assembled and compared with those of the wild relatives. The structure of cp genomes was highly conserved among cultivars and wild relatives. Phylogenetic analyses based on the assembled cp genomes showed that all chrysanthemum cultivars grouped together and shared 64 substitutions that were distinct from those of their wild relatives. These results indicated that a diverged lineage of the genus Chrysanthemum, which was most likely an extinct or un-sampled species/population, provided a maternal source for modern cultivars. These findings provide important insights into the origin of chrysanthemum cultivars, and a source of valuable genetic markers for chrysanthemum breeding programs.

Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1197) of microhomoloies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlight the importance of microhomology in mitochondrial genome evolution.