Jazlyn A Mooney’s research while affiliated with University of Southern California and other places

Characterizing genetic variation in natural populations is central to evolutionary biology. However, most non-model organisms lack integral genomic resources such as reference genomes and recombination maps, limiting accurate evolutionary inference. Here, we explore the consequences of reference genome bias on the inference of genetic diversity, demographic histories, and recombination rates using gray foxes (Urocyon cinereoargenteus), which, like most members of Canidae, are traditionally mapped to the dog (Canis lupus familiaris) reference genome. Whole genome sequence data from gray foxes were mapped to the gray fox reference genome and two heterospecific canid references (dog and Arctic fox; Vulpes lagopus). Our results reveal that reference bias significantly affects population genomic analyses. Mapping to the conspecific gray fox genome improved read pairing, increased detection of SNPs, especially rare variants, and reduced spurious variants. Estimates of nucleotide diversity (π) and genetic differentiation (FST) were higher using the gray fox genome. We observed that mapping to heterospecific references leads to underestimates of population sizes, distorted demographic trajectories, and more variable recombination rates. These effects are further complicated by population-specific biases, which vary in their magnitude and direction across populations, highlighting the need for tailored approaches to mitigate reference bias. Importantly, FST outlier detection also differed among references, affecting functional interpretations. Collectively, this work addresses a critical gap in the rapidly expanding field of non-model species genomics by demonstrating the importance of using conspecific genomic resources in evolutionary research and illustrating how reliance on distantly related reference genomes can distort population genetic analyses.

Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost‐effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low‐quality samples, and cost‐efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under‐powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user‐friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP‐level data, to design a successful and cost‐effective SNP panel for a diploid species of conservation concern.

Clonal hematopoiesis becomes increasingly common with age, but its cause is enigmatic because driver mutations are often absent. Serial observations infer weak selection indicating variants are acquired much earlier in life with unexplained initial growth spurts. Here we use fluctuating CpG methylation as a lineage marker to track stem cell clonal dynamics of hematopoiesis. We show, via the shared prenatal circulation of monozygotic twins, that weak selection conferred by stem cell variation created before birth can reliably yield clonal hematopoiesis later in life. Theory indicates weak selection will lead to dominance given enough time and large enough population sizes. Human hematopoiesis satisfies both these conditions. Stochastic loss of weakly selected variants is naturally prevented by the expansion of stem cell lineages during development. The dominance of stem cell clones created before birth is supported by blood fluctuating CpG methylation patterns that exhibit low correlation between unrelated individuals but are highly correlated between many elderly monozygotic twins. Therefore, clonal hematopoiesis driven by weak selection in later life appears to reflect variation created before birth.

The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on traits that may be less important in the domesticated context. Thus, here we hypothesize that strongly deleterious mutations may have become less deleterious in domesticated populations. We test this hypothesis by estimating the distribution of fitness effects (DFE) for new amino acid changing mutations using whole-genome sequence data from 24 gray wolves and 61 breed dogs. We find that the DFE is strikingly similar across canids, with 26-28% of new amino acid changing mutations being neutral/nearly neutral (| s| < 1e-5), and 41-48% under strong purifying selection (| s| > 1e-2). Our results are robust to different model assumptions suggesting that the DFE is stable across short evolutionary timescales, even in the face of putative drastic changes in the selective pressure caused by artificial selection during domestication and breed formation. On par with previous works describing DFE evolution, our data indicate that the DFE of amino acid changing mutations depends more strongly on genome structure and organismal characteristics, and less so on shifting selective pressures or environmental factors. Given the constant DFE and previous data showing that genetic variants that differentiate wolf and dog populations are enriched in regulatory elements, we speculate that domestication may have had a larger impact on regulatory variation than on amino acid changing mutations. Significance Statement Domestication of dogs to live alongside humans resulted in a dramatic shift in the pressures of natural selection. Thus, comparing dogs and wolves offers a unique opportunity to assess how these shifts in selective pressures have impacted the fitness effects of individual mutations. In this project, we use patterns of genetic variation in dogs and wolves to estimate the distribution of fitness effects (DFE), or the proportions of amino acid changing mutations with varying fitness effects throughout the genome. Overall, we find that the DFE for amino acid changing mutations is similar between dogs and wolves. Even genes thought to be most affected by domestication show a similar DFE, suggesting that the DFE has remained stable over evolutionary time.

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers ( Panthera tigris ), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as “Generic” tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25×) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex- and in situ populations.

Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favored for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for use in population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel user-friendly SNP selection pipeline for population assignment and individual identification, mPCRselect. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for species of conservation concern.

Runs of homozygosity (ROH) are genomic regions that arise when two copies of an identical ancestral haplotype are inherited from parents with a recent common ancestor. In this study, we performed a novel comprehensive analysis to infer genetic diversity among dogs and quantified the association between ROH and non-disease phenotypes. We found distinct patterns of genetic diversity across clades of breed dogs and elevated levels of long ROH, compared to non-domesticated dogs. These high levels of FROH (inbreeding coefficient) are a consequence of recent inbreeding among domesticated dogs during breed establishment. We identified statistically significant associations between FROH and height, weight, lifespan, muscled, white head, white chest, furnish, and length of fur. After correcting for population structure, we identified more than 45 genes across the three examined quantitative traits that exceeded the threshold for suggestive significance, indicating significant polygenic inheritance for the complex quantitative phenotypes in dogs.

Scaling is a common practice in population genetic simulations to increase computational efficiency. However, there exists a dearth of standardized guidelines for best practices. Few studies have examined the effects of scaling on diversity and whether the results are directly comparable to unscaled and empirical data. We examine the effects of scaling in two model populations, modern humans and Drosophila melanogaster . The reason is twofold: 1) due to the substantial difference in population sizes and generation times, human populations require moderate-to-no scaling, while more dramatic scaling is required for Drosophila ; and 2) model populations have empirical data for comparison. We determine whether coalescence, runtime, memory, estimates of diversity, the site frequency spectra, and deleterious variation are affected by scaling. We also explore the effect of varying the simulated segment length and burn-in times. We find that the typical 10N generation burn-in is often not sufficient for full coalescence to occur in human or Drosophila simulations. As expected, memory and runtime increase as the scaling coefficient decreases and the length of the simulated segment increases. We show that simulating larger segments in humans is preferable, as it produces a smaller variance in diversity estimates. Conversely, in Drosophila it is preferable to simulate smaller segments and concatenate them into full genome for achieving comparable levels of diversity to empirical data. We find that aggressive scaling leads to stronger negative selection and ultimately amplifies the strength of background selection on flanking variation. Author Summary Scaling is a common approach to make population genetic simulations more computationally tractable. However, the implications of scaling and best practices for scaling are still unknown. This study highlights the importance of carefully considering scaling practices for forward-in-time population genetics simulations. We provide insights about the trade-offs between computational efficiency and accuracy of scaled simulations relative to empirical data, in human and Drosophila . We achieved this by varying the species demographic model; the method of coalescence; the simulated genomic element length; and the scaling factor. For each combination of parameters genetic diversity was quantified and computational was efficiency tracked. Our findings suggest that when simulating populations, such as humans, where moderate scaling is required, one should simulate larger genomic segments for more accurate measures of diversity. Scaling seems to cause an inflation of diversity in human simulations relative to empirical data. On the other hand, in populations where more aggressive scaling is required, such as Drosophila , simulating smaller segments is advantageous. The scaling factor increases substantially in Drosophila studies, and the simulated data experiences a drastic drop in diversity, relative to empirical data, and an increased effect of purifying selection.

Clonal hematopoiesis becomes increasingly common with age, but its cause is enigmatic because driver mutations are often absent. Serial observations infer weak selection indicating variants are acquired much earlier in life with unexplained initial growth spurts. Here we use fluctuating CpG methylation as a lineage marker to track stem cell clonal dynamics of hematopoiesis. We show, via the shared prenatal circulation of monozygotic twins, that weak selection conferred by stem cell variation created before birth can reliably yield clonal hematopoiesis later in life. Theory indicates weak selection will lead to dominance given enough time and large enough population sizes. Human hematopoiesis satisfies both these conditions. Stochastic loss of weakly selected variants is naturally prevented by the expansion of stem cell lineages during development. The dominance of stem cell clones created before birth is supported by blood fluctuating CpG methylation patterns that exhibit low correlation between unrelated individuals but are highly correlated between many elderly monozygotic twins. Therefore, clonal hematopoiesis driven by weak selection in later life appears to reflect variation created before birth.

Reference genome assemblies have been created from multiple lineages within the Canidae family, however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases (Mb), respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern US and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.