A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis.

The deciduous Chinese tupelo (Nyssa sinensis Oliv.) is a popular ornamental tree for the spectacular autumn leaf color. Here, using single-molecule sequencing and chromosome conformation capture data, we report a high-quality, chromosome-level genome assembly of N. sinensis. PacBio long reads were de novo assembled into 647 polished contigs with a total length of 1,001.42 megabases (Mb) and an N50 size of 3.62 Mb, which is in line with genome sizes estimated using flow cytometry and the k-mer analysis. These contigs were further clustered and ordered into 22 pseudo-chromosomes based on Hi-C data, matching the chromosome counts in Nyssa obtained from previous cytological studies. In addition, a total of 664.91 Mb of repetitive elements were identified and a total of 37,884 protein-coding genes were predicted in the genome of N. sinensis. All data were deposited in publicly available repositories, and should be a valuable resource for genomics, evolution, and conservation biology.

Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling.

Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.

Optimal control and cold war dynamics between plant and herbivore.

Herbivores eat the leaves that a plant needs for photosynthesis. However, the degree of antagonism between plant and herbivore may depend critically on the timing of their interactions and the intrinsic value of a leaf. We present a model that investigates whether and when the timing of plant defense and herbivore feeding activity can be optimized by evolution so that their interactions can move from antagonistic to neutral. We assume that temporal changes in environmental conditions will affect intrinsic leaf value, measured as potential carbon gain. Using optimal-control theory, we model herbivore evolution, first in response to fixed plant strategies and then under coevolutionary dynamics in which the plant also evolves in response to the herbivore. In the latter case, we solve for the evolutionarily stable strategies of plant defense induction and herbivore hatching rate under different ecological conditions. Our results suggest that the optimal strategies for both plant and herbivore are to avoid direct conflict. As long as the plant has the capability for moderately lethal defense, the herbivore will modify its hatching rate to avoid plant defenses, and the plant will never have to use them. Insights from this model offer a possible solution to the paradox of sublethal defenses and provide a mechanism for stable plant-herbivore interactions without the need for natural enemy control.