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.

In theory, genomic erosion can be reduced in fragile “recipient” populations by translocating individuals from genetically diverse “donor” populations. However, recent simulation studies have argued that such translocations can, in principle, serve as a conduit for new deleterious mutations to enter recipient populations. A reduction in evolutionary fitness is associated with a higher load of deleterious mutations and thus, a better understanding of evolutionary processes driving the empirical distribution of deleterious mutations is crucial. Here, we show that genetic load is evolutionarily dynamic in nature and that demographic history greatly influences the distribution of deleterious mutations over time. Our analyses, based on both demographically explicit simulations as well as whole genome sequences of potential donor-recipient pairs of Montezuma Quail (Cyrtonyx montezumae) populations, indicate that all populations tend to lose deleterious mutations during bottlenecks, but that genetic purging is pronounced in smaller populations with stronger bottlenecks. Despite carrying relatively fewer deleterious mutations, we demonstrate how small, isolated populations are more likely to suffer inbreeding depression as deleterious mutations that escape purging are homogenized due to drift, inbreeding, and ineffective purifying selection. We apply a population genomics framework to showcase how the phylogeography and historical demography of a given species can enlighten genetic rescue efforts. Our data suggest that small, inbred populations should benefit the most when assisted gene flow stems from genetically diverse donor populations that have the lowest proportion of deleterious mutations.

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.

Populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity (i.e., higher adaptive potential) to respond to ecological stressors. We are interested in how the adaptive potential captured in protein-coding genes persists in small populations and how it fluctuates relative to overall genomic diversity. We analyzed individual whole genome sequences from different populations of Montezuma Quail (Cyrtonyx montezumae), a small ground-dwelling bird that is sustainably harvested in some portions of its range but is of conservation concern elsewhere. Our historical demographic results indicate that overall, Montezuma Quail populations in the U.S. exhibit low levels of genomic diversity due in large part to long-term declines in effective population sizes over nearly a million years. The smaller and more isolated Texas population is significantly more inbred than the large Arizona and the intermediate-sized New Mexico populations. The Texas gene pool has a significantly lower proportion of deleterious alleles than the Arizona gene pool, but also significantly more high-frequency deleterious alleles that, coupled with elevated inbreeding, elevate the realized genetic load in Texas. Our results highlight that although small, isolated populations can maintain adaptive potential (i.e., genic diversity can still be high), they are at higher risk of inbreeding depression as detrimental mutations rise in frequency due to drift and weakened purifying selection. Our study illustrates how population genomics can be used to proactively assess both neutral and adaptive aspects of contemporary genetic diversity in a conservation framework while simultaneously considering deeper demographic histories.

In principle, populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity (i.e., higher adaptive potential) to respond to ecological stressors. Small isolated populations tend to lose genetic diversity rapidly due to the detrimental effects of drift and inbreeding via genetic erosion. We are interested in how adaptive potential persists in small populations and how it fluctuates relative to overall genomic diversity. We analyzed individual whole genome sequences from different populations of Montezuma Quail (Cyrtonyx montezumae), a small ground-dwelling bird that is sustainably harvested in some portions of its range but is of conservation concern elsewhere. Our results indicate that overall, Montezuma Quail populations in the U.S. exhibit low levels of genomic diversity due in large part to long-term declines in effective population sizes over nearly a million years. The smaller and more isolated Texas population is significantly more inbred than the large Arizona and the intermediate-sized New Mexico populations. The Texas gene pool has a significantly lower proportion of deleterious alleles than the Arizona gene pool, but also significantly more high-frequency deleterious alleles that, coupled with elevated inbreeding, elevate the realized genetic load in Texas. Our results highlight that smaller, isolated populations are at higher risk of inbreeding depression as detrimental mutations rise in frequency due to drift and weakened purifying selection. Our study illustrates how population genomics can be used to proactively assess both neutral and adaptive aspects of contemporary genetic diversity in a conservation framework while simultaneously considering deeper demographic histories.