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Abstract Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334–127 Mb) representing macrochromosomes and 8 small scaffolds (63–22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic. 

Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and they are often found in close association with humans, domestic animals, and wildlife. Although a significant amount of research has focused on rodents’ prominence as known reservoirs of zoonotic viruses, there has been less emphasis on the viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate polyomaviruses in wild rodents from the Baja California peninsula, Mexico, using fecal samples. We identified a novel polyomavirus in fecal samples from two rodent species, a spiny pocket mouse (Chaetodipus spinatus) and a Dulzura kangaroo rat (Dipodomys simulans). These two polyomaviruses represent a new species in the genus Betapolyomavirus. Sequences of this polyomavirus cluster phylogenetically with those of other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the human respiratory tract. Through our continued work on seven species of rodents, we endeavor to explore the viral diversity associated with wild rodents on the Baja California peninsula and expand on current knowledge of rodent viral ecology and evolution. 

For nearly 30 years, biologists have documented a striking pattern of intra-species genetic divergence on the Baja California peninsula in dozens of disparate species. Evolutionary theory predicts that when such a pattern is shared among species the cause is extrinsic (e.g., environmental, climatic, physiographic, geological). The leading hypothesis within biological literature has been that genetic divergence was facilitated by flooding across the central peninsula by a seaway between ~3-1 Ma, resulting in separation of northern and southern populations. However, new detailed geologic mapping from the Baja GeoGenomics consortium reveals evidence for continuous terrestrial environments during the last ~30 Myr in a ≥40-km-wide ~E-W region of the central peninsula that straddles the modern-day crest, conclusively refuting the seaway hypothesis. Through integration of tectonic, volcanic, and sedimentological evidence with genomic (DNA) and gene expression (RNA) data for plants and animals, we are developing a new working model for Earth-life evolution on the peninsula over the last ~5 Myr. In this model, rift-related uplift drives the growth and dissection of topography, causing increased microenvironmental heterogeneity that populations differentially adapted to in the north and south. This is evidenced by widespread, statistically significant niche divergence in populations between northern and southern Baja in 21 studied taxa. This pattern is supported by strong differences in gene expression in northern and southern populations of two lizard species, particularly in genes relating to metabolism, which may indicate different diet or energy requirements between the regions. Habitats in the north and south then shifted due to glacial and interglacial periods, indicated by hindcasting the estimated niche conditions of those 21 taxa. With ongoing analyses, we expect to find genomic signatures of differential natural selection and adaptation within these species due in part to monsoon-driven rainfall differences. The significance of this work is twofold: it demonstrates the importance of incorporating geological data into evolutionary hypotheses and it cautions how mis-assigning cause-effect relationships in individual Earth-life systems can bias our fundamental understanding of how Earth processes shape biological evolution writ large. 

Abstract Kelp forests are globally important and highly productive ecosystems, yet their persistence and protection in the face of climate change and human activity are poorly known. Here, we present a 35-year time series of high-resolution satellite imagery that maps the distribution and persistence of giant kelp (Macrocystis pyrifera) forests along ten degrees of latitude in the Northeast Pacific Ocean. We find that although 7.7% of giant kelp is protected by marine reserves, when accounting for persistence only 4% of kelp is present and protected. Protection of giant kelp decreases southerly from 20.9% in Central California, USA, to less than 1% in Baja California, Mexico, which likely exacerbates kelp vulnerability to marine heatwaves in Baja California. We suggest that a two-fold increase in the area of kelp protected by marine reserves is needed to fully protect persistent kelp forests and that conservation of climate-refugia in Baja California should be a priority. 

Marine conservation design and fisheries management are increasingly integrating biophysical, socio-economic and governance considerations. Integrative approaches are adopted to achieve more effective, equitable, inclusive, and robust marine policies and practices. This paper describes a participatory process to co-produce biophysical, socio-economic, and governance principles to guide the design and management of marine reserves in three regions of Mexico: the Pacific region of the Baja California Peninsula, the Gulf of California, and the Mexican Caribbean. The process of co-producing the principles included convening a coordination team, reviewing the science, convening multi-stakeholder workshops, developing and communicating the principles with key practitioners and policy makers, and supporting uptake and application to policy and practice. Biophysical principles were related to: habitat representation and risk spreading; protecting critical, special and unique areas; incorporating connectivity; allowing time for recovery; adapting to changes in climate and ocean chemistry; and considering threats and opportunities. Socio-economic principles focused on: integrating the social context, local aspirations, and human-environment interactions; considering economic and non-economic uses, promoting an equitable distribution of costs and benefits, and respecting and maintaining cultural identity and diversity. Governance principles prioritized establishing and ensuring legitimacy and institutional continuity; implementing collaborative and adaptive management; and, promoting effective management. The paper also examines early efforts to implement the principles, next steps to promote further uptake and application in Mexico, and lessons learned from the process. Thus it provides insights into a practical process and a set of principles that are valuable to inform marine conservation and fisheries management processes elsewhere.