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Reproductive isolation is necessary for population divergence to lead to the formation of separate species. This can occur due to physical isolation of populations, which drives allopatric speciation, or other methods of isolation, such as sympatric speciation where the diverging species are physically in the same range, but structural genomic changes or mutations cause the population to diverge into two different species. Parapatric speciation occurs when populations that are geographically adjacent to each other diverge, which can be driven by adaptations to environmental differences, even with ongoing gene flow. Two desert- adapted brittlebush species, Encelia farinosa and Encelia californica, diverged less than 1 million years ago (Singhal et al., 2020) and have a parapatric distribution, residing in different environments in the Mojave and Sonoran deserts. Encelia farinosa (Brittlebush) has unique silvery leaves that are covered in tiny hairs (leaf pubescence) to better control leaf temperature in the hot and arid conditions of the Sonoran Desert. Encelia californica (California Brittlebush) does not display leaf pubescence and is found in a smaller region of the Mediterranean-like environment of the west coast of North America. Encelia californica is exposed to more precipitation than most other Encelia species. Even with their different morphologies, these two species are still able to hybridize and create fertile offspring (Clark, 1998). Using PacBio sequencing and Hi-C scaffolding, we assembled and annotated reference genomes for both species to investigate the genomic basis of reproductive isolation in these two species. The scaffold N50/L50 are 10 scaffolds and 76.3 Mbp, and 12 scaffolds and 64.5 Mbp for E. farinosa and E. californica, respectively. Using comparative genomic analyses such as tests for differential adaptation and chromosomal translocations will help reveal whether the drivers of speciation in the Encelia radiation were external (e.g., geologic/climatic) or internal (e.g., genomic rearrangement). These analyses will also help answer how accumulated genomic differences can cause speciation in populations that are not geographically isolated. Analyses such as these are new, exciting sources of information for testing geogenomic and other Earth- life hypotheses. 

Understanding the timescales on which different geologic processes influence genetic divergence is crucial to defining and testing geogenomic hypotheses and characterizing Earth- life evolution. To see if we can recover a genetic signal produced by a hypothetical physical barrier to gene flow, we used a geographically explicit simulation approach. We used the CDMetaPop software to simulate heritable genetic, nonadaptive, data for 20 geographically distinct populations distributed throughout the Baja California peninsula of Mexico, a landscape where a transpeninsular seaway barrier has been proposed to have isolated the southern peninsula and caused the observed latitudinal genetic divergence in over 80 terrestrial species. We simulated 10,000 generations of isolation by a barrier under two dispersal scenarios (1 km and 100 km of max. dispersal from population of origin per generation) and three DNA substitution rates (10-7, 10-8 and 10-9 nucleotide substitutions per site per generation). Our simulations indicate that a physical barrier can produce strong genetic divergence within 10,000 generations, comparable to the continuum of values observed in nature for different taxonomic groups and geological settings. We found that the generation time of the organism was by far the most important factor dictating the rate of divergence. Evaluating different generation times (0.02, 0.2, 2 and 20 years), showed that species with longer generation times require longer periods of isolation to accumulate genetic divergence over 10k generations (~1 My). Simulating 10,000 generations of gene flow following removal of the barrier showed that the divergence signal eroded quickly, in less than 1,000 generations in every scenario, a pattern supported by theory from population genetics. These results are particularly relevant to geogenomic studies because they show that ephemeral gene flow barriers produce different magnitudes of genetic signals depending on attributes of the organism, particularly generation time, and that if reproductive isolation is not achieved during isolation, then the evolutionary signal of an ephemeral barrier may not develop. This work helps guide the limits of detectability when integrating genomic data with geological and climatic processes. 

Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.