The California ribbed mussel, Mytilus californianus, is an ecosystem engineer crucial for the survival of many marine species inhabiting the intertidal zone of California. Here, we describe the first reference genome for M. californianus and compare it to previously published genomes from three other Mytilus species: M. edulis, M. coruscus, and M. galloprovincialis. The M. californianus reference genome is 1.65 Gb in length, with N50 sequence length of 118Mb, and an estimated 86.0% complete single copy genes. Compared to the other three Mytilus species, the M. californianus genome assembly is the longest, has the highest N50 value, and the highest percentage complete single copy genes. This high-quality genome assembly provides a foundation for population genetic analyses that will give insight into future conservation work along the coast of California.

The rubber boa, Charina bottae is a semi-fossorial, cold-temperature adapted snake that ranges across the wetter and cooler ecoregions of the California Floristic Province. The rubber boa is one of two species in the family Boidae native to California and currently has two recognized subspecies, the Northern rubber boa Charina b. bottae and the Southern rubber boa C. b. umbratica. Recent genomic work on Charina bottae indicate that these two subspecies are collectively composed of four divergent lineages that separated during the late Miocene. Analysis of habitat suitability indicate that C. bottae umbratica montane sky-island populations from southern California will lose the majority of their habit over the next 70 years, and is listed as Threatened under the California Endangered Species Act. Here, we report a new, chromosome-level assembly of C. bottae bottae as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome 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 289 scaffolds covering 1,804,944,895 base pairs, has a contig N50 of 37.3 Mb, a scaffold N50 of 97 Mb, and BUSCO completeness score of 96.3%, and represents the first reference genome for the Boidae snake family. This genome will enable studies of genetic differentiation and connectivity among C. bottae bottae and C. bottae umbratica populations across California and help manage locally endemic lineages as they confront challenges from human induced climate warming, droughts, and wildfires across California.

Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. We used Pacific Biosciences HiFi long sequencing reads, and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly of 550Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6Mb and a scaffold N50 of 21.4Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the sister species P. ochraceus in size and completeness. Both Pisaster assemblies are consistent with previously published karyotyping results showing sea star genomes are organized into 22 autosomes. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.

Biodiversity monitoring in conservation projects is essential to understand environmental status and recovery. However, traditional field surveys can be biased towards visual detection and/or focused on measuring the biodiversity of a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has the potential to sample a taxonomically broader set of organisms with similar effort, but these approaches are still in the early stages of development and testing. Here, we explore the utility of multilocus eDNA metabarcoding to explore the impact on local biodiversity of removal of the red swamp crayfish, a globally invasive species, from a desert oasis ecosystem. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity changes of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish in control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes. Metabarcoding of the 16S (targeting prokaryotes) and the ITS1 (targeting fungi) loci in the invaded oasis and tanks pre-removal were, however, successful in discerning a suite of 90 crayfish-associated taxa to serve as candidate bioindicators of invasive presence. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish-associations in the literature, we support 9 taxa to be high-ranking, and suggest they be prioritized in future biomonitoring. Biodiversity analyses from five metabarcode loci including plants, animals, and both prokaryotic and eukaryotic microbes showed that communities differed but that species richness remained relatively similar between oases through time. Our results reveal that, while there are limitations of eDNA approaches to detect crayfish and other invasive species, microbial bioindicators offer a largely untapped biomonitoring opportunity for invasive species management, adding a valuable resource to a conservation manager’s toolkit.

Biodiversity monitoring in conservation projects is essential to understand environmental health, complexity, and recovery. However, traditional field surveys can be expensive, time‐consuming, biased toward visual detection, and/or only measure a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has the potential to sample a taxonomically broader set of organisms with a similar effort, but many of these approaches are still in the early stages of development and testing. Here, we used multi‐locus eDNA metabarcoding to understand how the removal of invasive red swamp crayfish using cypermethrin pesticide impacts local biodiversity of a desert oasis ecosystem, as well as to detect crayfish both directly and indirectly. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish directly in either control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes, similar to previous studies which have shown variable levels of success in detecting crayfish from environmental samples. However, we were successful in discerning a suite of 90 crayfish‐associated taxa to serve as candidate bioindicators of invasive presence using 16S and fungal ITS2 metabarcoding. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish associations in the literature, we support nine taxa to be high ranking, and suggest they be prioritized in future biomonitoring. Biodiversity analyses from five metabarcode loci including plants, animals, and both prokaryotic and eukaryotic microbes showed that communities differed but that species richness remained relatively similar between oases through time. Our results reveal that, while there are limitations of eDNA approaches to detect crayfish and other invasive species, microbial bioindicators offer a largely untapped biomonitoring opportunity for invasive species management, adding a valuable resource to a conservation manager's toolkit.