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Abstract Mimulus laciniatus (syn. Erythranthe lacinata) is an annual plant endemic to the Sierra Nevada region of California. Mimulus laciniatus is notable for its specialized ecological niche, thriving in granite outcrops of alpine environments characterized by shallow soils that dry out rapidly as the snowpack is exhausted during season-ending droughts. Due to its narrow habitat range and sensitivity to environmental change, this species serves as an important model for studying adaptation and survival in marginal habitats. As part of the California Conservation Genomics Project, here we report the sequencing and assembly of a high-quality nuclear genome and chloroplast genome of M. laciniatus. The primary assembly is 309.96 Mb and consists of 104 scaffolds with a scaffold N50 of 20.99 Mb, a largest contig size of 24.29 Mb and a contig N50 of 11.09 Mb, The alternate haplotype assembly consists of 194 scaffolds spanning 213.84 Mb. BUSCO completeness of the primary assembly is 98.6%. This high quality genome adds a valuable resource to the expanding collection of sequenced genomes of the monkeyflowers (Mimulus sensu lato), which have become a model clade for studying ecological adaptation, speciation, and evolutionary genetics. 

Abstract Reconstructions of evolutionary history can be restricted by a lack of high-quality reference genomes. To date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species—the sun, sloth, and Andean bears—and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Multiple divergence dating approaches suggest that the six Ursine bears likely diversified in the last 5 Ma, but that divergence times within Ursinae are significantly impacted by gene tree heterogeneity. Consistent with this, we observe that nearly 50% of gene trees conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the karyotype of Ursinae is largely similar to the ancestral karyotype of all bears twenty million years prior. In contrast to this conservation of structure, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and Andean bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified. 

Abstract Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus conservation efforts on watersheds with high levels of genetic diversity, local adaptation, and even cryptic endemism. Here, as part of the California Conservation Genomics Project (CCGP), we report the first reference genome for the American rubyspot damselfly, Hetaerina americana, a species associated with springs, streams and rivers throughout California. Following the CCGP assembly pipeline, we produced two de novo genome assemblies. The primary assembly includes 1,630,044,487 base pairs, with a contig N50 of 5.4 Mb, a scaffold N50 of 86.2 Mb, and a BUSCO completeness score of 97.6%. This is the seventh Odonata genome to be made publicly available and the first for the subfamily Hetaerininae. This reference genome fills an important phylogenetic gap in our understanding of Odonata genome evolution, and provides a genomic resource for a host of interesting ecological, evolutionary, and conservation questions for which the rubyspot damselfly genus Hetaerina is an important model system. 

Abstract Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California. 

Abstract Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.