The Inyo County population of California towhee, now recognized as Melozone crissalis, was officially listed as Threatened under the U.S. Endangered Species Act in 1987. This isolated population in the Argus Mountains was then estimated to consist of less than 175 individuals. Its major threats were habitat destruction caused by grazing, mining, water exporting, and human recreational activities but stakeholders eventually developed a recovery plan to mitigate habitat damage. Due to the demographic success of the recovery plan, the U.S. Fish and Wildlife Service (USFWS) proposed to remove the California towhee from their formal list of threatened and endangered species in 2013. Herein, we generated a high-quality reference genome assembly for a typical representative of the California towhee (N50 = 22 Mb among 627 contigs, max contig size 89.1Mb), then conducted whole genome resequencing on birds sampled from geographic sites across much of the species’ range. Our findings indicate that the California towhee gene pool is relatively deep (i.e., diverse; mean individual heterozygosity = 0.0021, range = 0.0013-0.0026) and that moderately low levels of autozygosity in isolated populations are due to a combination of historic and contemporary inbreeding. Our population, landscape, and phylogeographic analyses indicate that the shallower (less diverse) regions of the gene pool are likely due to a combination of natural geography, anthropogenic impacts, and demographic histories associated with isolated habitats. None of our findings are inconsistent with the 2013 USFWS proposal and we see no reason to protest the delisting petition based exclusively on genetic/genomic data.

The White Sands pupfish (Cyprinodon tularosa), endemic to New Mexico in Southwestern North America, is of conservation concern due in part to invasive species, chemical pollution, and groundwater withdrawal. Herein, we developed a high quality draft reference genome and use it to provide biological insights into the evolution and conservation of C. tularosa. Specifically, we localized microsatellite markers previously used to demarcate Evolutionary Significant Units, evaluated the possibility of introgression into the C. tularosa genome, and compared genomic diversity among related species. The de novo assembly of PacBio Sequel II error-corrected reads resulted in a 1.08Gb draft genome with a contig N50 of 1.4Mb and 25,260 annotated protein coding genes, including 95% of the expected Actinopterigii conserved orthologs. Many of the previously described C. tularosa microsatellite markers fell within or near genes and exhibited a pattern of increased heterozygosity near genic areas compared to those in intergenic regions. Genetic distances between C. tularosa and the widespread invasive species C. variegatus, which diverged ~1.6-4.7 MYA, were 0.027 (nuclear) and 0.022 (mitochondrial). Nuclear alignments revealed putative tracts of introgression that merit further investigation. Genome-wide heterozygosity was markedly lower in C. tularosa compared to estimates from related species, likely because of smaller long-term effective population sizes constrained by their isolated and limited habitat. These population inferences, generated from our new genome assembly, provide insights into the long term and contemporary White Sands pupfish populations that are integral to future management efforts.