Improved estimation of climate niches is critical, given climate change. Plant adaptation to climate depends on their physiological traits and their distributions, yet traits are rarely used to inform the estimation of species climate niches, and the power of a trait‐based approach has been controversial, given the many ecological factors and methodological issues that may result in decoupling of species' traits from their native climate. For 107 species across six ecosystems of California, we tested the hypothesis that mechanistic leaf and wood traits can robustly predict the mean of diverse species' climate distributions, when combining methodological improvements from previous studies, including standard trait measurements and sampling plants growing together at few sites. Further, we introduce an approach to quantify species' trait‐climate mismatch. We demonstrate a strong power to predict species mean climate from traits. As hypothesized, the prediction of species mean climate is stronger (and mismatch lower) when traits are sampled for individuals closer to species' mean climates. Improved resolution of species' climate niches based on mechanistic traits can importantly inform conservation of vulnerable species under the threat of climatic shifts in upcoming decades. Read the free Plain Language Summary for this article on the Journal blog.

Sandblossoms, Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and metrics to describe the genetic structure of natural populations. Despite the importance of L. parryae in the development of landscape genetics and phylogeography, there are no genomic resources available for the species. Through the California Conservation Genomics Project, we assembled the first genome in the genus Linanthus. Using PacBio HiFi long reads and Hi-C chromatin conformation capture, we assembled 123 scaffolds spanning 1.51 Gb of the 1.96 Gb estimated genome, with a contig N50 of 18.7 Mb and a scaffold N50 of 124.8 Mb. This assembly, with a BUSCO completeness score of 88.7%, will allow us to revisit foundational ideas central to our understanding of how evolutionary forces operate in a geographic landscape. In addition, it will be a new resource to uncover adaptations to arid environments in the fragile desert habitat threatened by urban and solar farm development, climate change, and off-road vehicles.

Premise: Understanding how plants successfully diversified in novel environments is a central question in evolutionary biology. Linanthus occurs in arid areas of western North America and exhibits extensive floral trait variation, multiple color polymorphisms, differences in blooming time, and variation in life history strategies. We reconstructed the evolutionary history of this genus.Methods: We generated restriction‐site associated (ddRAD) sequences for 180 individuals and target capture (TC) sequences for 63 individuals, with complete species sampling. Using maximum likelihood and pseudo‐coalescent approaches, we inferred phylogenies of Linanthus and used them to model the evolution of phenotypic traits and investigate the genus's geographic speciation history.Results: Relationships are consistent and well supported with both ddRAD and TC data. Most species are monophyletic despite extensive local sympatry and range overlap, suggesting strong isolating barriers. The non‐monophyly of the night‐blooming and perennial species may be due to rapid speciation or cryptic diversity. Perenniality likely evolved from annuality, a rare shift in angiosperms. Night‐blooming evolved three times independently. Flower color polymorphism is an evolutionarily labile trait that is likely ancestral. No single geographic mode of speciation characterizes this diversification, but most species overlap in range, which suggests that they evolved in parapatry.Conclusions: Our results illustrate the complexity of phylogenetic inference for recent radiations, even with multiple sources of genomic data and extensive sampling. This analysis provides a foundation for understanding aridity adaptations, such as evolution of flower color polymorphisms, night‐blooming, and perenniality, as well as speciation mechanisms.

Premise: Understanding how arid-adapted plants have diversified in harsh environments is a central question in evolutionary biology. Linanthus (Polemoniaceae) occurs in biodiverse dry areas of Western North America and exhibits extensive floral trait variation, multiple color polymorphisms, differences in blooming time, and variation in life history strategies. Here, we reconstruct the evolutionary history of this group. Methods: We generated restriction-site associated (ddRAD) sequences for 180 individuals and target capture (TC) sequences for 63 individuals, with complete species sampling. Using maximum likelihood and pseudo-coalescent approaches, we inferred phylogenies of Linanthus and used these phylogenies to model the evolution of phenotypic traits and investigate the geographic speciation history of this genus. Key results: Shallow relationships are consistent and well supported with both ddRAD and TC data. Most species are monophyletic despite rampant local sympatry and range overlap, suggesting strong isolating barriers. The non-monophyly of some species is possibly due to rapid speciation or issues with current species delimitation. Perenniality likely evolved from annuality, a rare shift in angiosperms. Night blooming evolved three times independently. Flower color polymorphism is an evolutionarily labile trait and is likely ancestral. No single geographic mode of speciation characterizes the radiation but most species overlap in range, suggesting they evolved in parapatry. Conclusions: Our results illustrate the complexity of phylogenetic inference for recent radiations, even with multiple sources of genomic data and extensive sampling. This analysis provides a foundation to understand aridity adaptations, such as evolution of flower color polymorphisms, night blooming, and perenniality, as well as speciation mechanisms.