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Abstract Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non‐model systems has also enabled a shift away from population‐based sampling to individual‐based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual‐based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population‐based sampling to individual‐based sampling schemes. Here, we discuss the benefits of individual‐based sampling for conservation and describe how landscape genomic methods, paired with individual‐based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user‐friendly, open‐source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). Thealgatrpackage includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology. 

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. 

Abstract Understanding the drivers of spatial patterns of genomic diversity has emerged as a major goal of evolutionary genetics. The flexibility of forward-time simulation makes it especially valuable for these efforts, allowing for the simulation of arbitrarily complex scenarios in a way that mimics how real populations evolve. Here, we present Geonomics, a Python package for performing complex, spatially explicit, landscape genomic simulations with full spatial pedigrees that dramatically reduces user workload yet remains customizable and extensible because it is embedded within a popular, general-purpose language. We show that Geonomics results are consistent with expectations for a variety of validation tests based on classic models in population genetics and then demonstrate its utility and flexibility with a trio of more complex simulation scenarios that feature polygenic selection, selection on multiple traits, simulation on complex landscapes, and nonstationary environmental change. We then discuss runtime, which is primarily sensitive to landscape raster size, memory usage, which is primarily sensitive to maximum population size and recombination rate, and other caveats related to the model’s methods for approximating recombination and movement. Taken together, our tests and demonstrations show that Geonomics provides an efficient and robust platform for population genomic simulations that capture complex spatial and evolutionary dynamics. 

Abstract Genetic diversity plays a key role in maintaining population viability by preventing inbreeding depression and providing the building blocks for adaptation. Understanding how genetic diversity varies across space is, therefore, of key interest in conservation and population genetics.Here, we introducewingen, anrpackage for calculating continuous maps of genetic diversity, including nucleotide diversity, allelic richness, and heterozygosity, from standard genotypic and spatial data using a spatial moving window approach. We provide functions to account for variation in sample size across space using rarefaction, to create kriging‐interpolated maps of genetic diversity, and to mask any areas that are outside the area of interest.Tests with simulated and empirical datasets demonstrate thatwingencan successfully capture variation in genetic diversity across landscapes from both reduced‐representation and whole genome sequencing datasets. For reduced‐representation datasets,wingen's functions can be run easily on a standard laptop computer, and we provide options for parallelization to increase the efficiency of running larger whole genome datasets.wingenprovides novel and computationally tractable tools for creating informative maps of genetic diversity with applications for conservation prioritization as well as population and landscape genetic analyses.