Summary: Multispecies interbreeding networks, or syngameons, have been increasingly reported in natural systems. However, the formation, structure, and maintenance of syngameons have received little attention. Through gene flow, syngameons can increase genetic diversity, facilitate the colonization of new environments, and contribute to hybrid speciation. In this study, we evaluated the history, patterns, and consequences of hybridization in a pinyon pine syngameon using morphological and genomic data to assess genetic structure, demographic history, and geographic and climatic data to determine niche differentiation. We demonstrated thatPinus edulis, a dominant species in the Southwestern US and a barometer of climate change, is a core participant in the syngameon, involved in the formation of two drought‐adapted hybrid lineages including the parapatric and taxonomically controversialfallax‐type. We found that species remain morphologically and genetically distinct at range cores, maintaining species boundaries while undergoing extensive gene flow in areas of sympatry at range peripheries. Our study shows that sequential hybridization may have caused relatively rapid speciation and facilitated the colonization of different niches, resulting in the rapid formation of two new lineages. Participation in the syngameon may allow adaptive traits to be introgressed across species barriers and provide the changes needed to survive future climate scenarios.

Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.

Background and Aims: Pinyon pine hybridization is widely acknowledged, but the frequency of and contributors to such interspecific mating remain largely unstudied. Pinus quadrifolia has three to four needles per fascicle, suggesting that it is a result of hybridization between the five-needled P. juarezensis and the single-needled P. monophylla. In this study we address the taxonomic validity of P. juarezensis, the hybrid origin of P. quadrifolia and the presence of hybridization and intermediate morphology as a result of interspecific hybridization in this complex.Methods: We address these questions by combining a genomic and morphological approach. We generated 1868 single nucleotide polymorphisms (SNPs) to detect genetic clusters using principal co-ordinates analyis, discriminant analysis of principal components, fastSTRUCTURE and ADMIXTURE analyses, and performed a morphological analysis of the leaves.Key Results: We found that the five-needled pinyons did not differ genetically from the four-needled P. quadrifolia, reducing the status of P. juarezensis to P. quadrifolia. We also found no evidence that P. quadrifolia is of hybrid origin from P. juarezensis × P. monophylla but is instead a genetically distinct species with natural needle number variation that has yet to be explained. Hybridization does occur in this complex, but mostly between P. quadrifolia and P. californiarum, and less commonly between P. quadrifolia and P. monophylla. Interestingly, some hybrid derivatives were detected between both single-needled taxa, P. monophylla and P. californiarum, a hybrid combination that has not yet been proposed. Hybrids have intermediate morphology when they have similar genetic contributions from both parental species; however, when one parent contributes more, hybrid derivatives resemble the parent with higher genetic contribution, resulting in cryptic introgression.Conclusions: Our detailed sampling across the distribution of this complex allows us to describe the patterns of hybridization among these taxa, resolves an ancient taxonomic conflict and provides insights into the challenges of exclusively using morphological traits when identifying these taxa with cryptic hybridization and variable morphology.

Habitat destruction and climate change are two primary drivers of global biodiversity loss. Many contemporary ecological preserves and preserve networks are designed to protect species and the ecological and evolutionary processes that will maintain future biodiversity. However, it is challenging to identify where to locate preserves and how to manage them to meet these goals. One emerging conservation tool is landscape genomics, which allows us to identify populations that may be maladapted to future climate and thereby helps prioritize areas for acquisition (areas of high adaptedness), restoration (areas of low adaptedness), and management. Here, using whole genome sequence data of 171 adult trees, we studied the climate adaptedness of California populations of coast live oak ( Quercus agrifolia ), a foundation species that broadly supports biodiversity, to develop a conservation management strategy, including direct acquisition, land management, and restoration that addresses the predicted impact of future climate. Over the range of coast live oak, we find that the northernmost and southernmost stands are predicted to be more at risk for maladaptation to climate change, with the central coast of California containing stands with high adaptedness, including in unprotected areas that might benefit from protection. Using three large preserves (focal sites) managed by The Nature Conservancy (TNC), we illustrate how moving seeds from low to high elevation parts of preserves could benefit future populations range‐wide by increasing overall climate adaptedness. We discuss the different levels of risk across focal sites and apply our interpretations into TNC's 400,000 + −acre conservation holdings in California to sustain future populations of this foundational tree species. This study represents a unique collaboration between academic and applied conservation scientists to both assess levels of maladaptedness of a foundational tree to predicted climate change and also develop a genomic‐informed seed transfer program to improve adaptedness of future populations.

Environmental factors shape the distributions of organisms and their underlying patterns of genetic variation. When climate changes rapidly, organisms that are adapted to current environments may become maladapted to future climates. Long‐lived tree species are especially susceptible to climate maladaptation due to their sessile nature and long generation times. Understanding how foundational tree species will respond to future climate, both in adaptive ability and distribution shifts, is imperative for effective management and conservation of tree populations and the ecosystems they comprise. Here, we used whole genome sequences from 163 individuals of blue oak ( Quercus douglasii ) to determine predicted adaptedness, the degree to which an organism can survive and reproduce in future climate, based on landscape genomic models, compare those genomic predictions with ecological niche model predictions, and propose seed sourcing and restoration site strategies to increase the adaptedness of stands at preserves managed by The Nature Conservancy. Both ecological and genomic models predict that blue oak stands will be more susceptible to future climate along the Sierra Nevada basin, with patches of higher climate adaptedness along the central coast of California. To test whether management practices could increase adaptedness of blue oak stands, we examined the impact of seed source and restoration site choice on future stands. Regardless of restoration site category, our expectation held true that future maladaptation risk is reduced the most when using seed sources preadapted to the future climate of the restoration site. However, restoration sites containing stands with high habitat suitability and high climate adaptedness always did best. We conclude that strategic conservation and management strategies utilizing seed transfer from climate‐adapted stands may improve the future health of blue oak stands susceptible to future climate.