Biology subjects

Phifer-Rixey, M.

Publications and source records attributed to Phifer-Rixey, M..

6 recordsLinked to original sources

bioRxiv2026

Body size and cranial shape differentiation in urban and rural house mice (Mus musculus domesticus)

Cities are characterized by elevated temperatures, increased pollution, and high-density human populations which often are accompanied by changes in available resources, like food. These shifts have the potential to drive phenotypic divergence in urban wildlife. Functional morphological traits, like body size, can mediate interactions between wildlife and habitat and are closely tied to life history and fitness. While examples of functional morphological variation associated with urbanization are increasing, variation in such traits as a response to urbanization remains unexplored for most taxa. Here, we investigated morphological divergence between urban and rural populations of house mice (Mus musculus domesticus). House mice are globally distributed in diverse habitats and are a model system with a wealth of phenotypic data, making them useful for the study of the impacts of urbanization on morphology. Using a paired replicate design, we sampled urban and rural populations in three distinct metropolitan regions in the eastern United States. We found that body size was smaller in urban populations. Using 3D geometric morphometrics, we also analyzed variation in cranial shape across habitats. Differences in cranial shape were largely allometric, that is, driven by differences in body size. However, we also uncovered evidence of cranial shape variation between habitats not explained by size. In contrast, we did not find evidence for habitat-driven differences in cranial capacity independent of size. Overall, our results suggest a key role for body size in mediating morphological responses to urbanization and highlight the potential of house mice as a globally-distributed model for urbanization.

zoology↗

bioRxiv2026

Dietary and gut microbial variation among urban and rural populations of house mice (Mus musculus domesticus)

Urbanization can result in shifts in abiotic and biotic factors, including temperature, pollution, habitat type, pathogens, and diet, among others. These shifts can, in turn, shape the ecological and evolutionary trajectory of urban wildlife. The gut microbiota has the potential to mediate host-environment interactions, especially in the context of diet and disease, and thus may be a useful lens for understanding the impacts of urbanization. House mice (Mus musculus domesticus) are a cosmopolitan human commensal with a wealth of genomic and metagenomic resources. Here, we investigate patterns of variation in diet and gut microbial diversity, community composition, and function using a paired urban-rural sampling design in house mice from three metro regions in the eastern United States. First, using stable isotope analysis, we found that habitat--urban versus rural--was a major driver of variation in {delta}15N, suggesting a diet richer in animal proteins in cities. Next, using short-read sequencing of the 16S rRNA gene, we found that urban mice have lower gut microbial taxonomic diversity than their rural counterparts. We also found that community composition varied among urban and rural habitats, with differences largely reflecting shifts among closely related taxa. In particular, Prevotellaceae, a family known to be responsive to dietary quality, was differentially abundant, with lower abundance in urban habitats. Finally, we found differentiation in a few predicted microbial functions across habitat, primarily related to metabolism. Together, data across three independent sampling regions provide strong evidence that urbanization has the potential to shape the diet and the microbiome of house mice.

microbiology↗

bioRxiv2025

Alternative splicing contributes to plasticity and regulatory divergence in locally adapted house mice from the Americas

Alternative splicing is a major driver of transcriptome and proteome variation, but the role of alternative splicing in regulatory evolution remains understudied. Alternative splicing can also contribute to phenotypic plasticity, which may be critical when taxa colonize new environments. Here, we investigate variation in alternative splicing among new wild-derived strains of mice from different climates in the Americas on both a standard and high-fat diet. We show that alternative splicing is widespread and highly context-dependent. Comparisons between strains on different diets revealed abundant gene-by-environment interactions affecting alternative splicing, with most genes showing strain- and sex-specific diet responses. More often than not, genes that were differentially spliced between strains were not differentially expressed, adding to evidence that the two regulatory mechanisms often act independently. Moreover, differentially spliced genes were more widely expressed across tissues but also less central to biological networks than differentially expressed genes, suggesting differences in pleiotropic constraint. Importantly, divergence in alternative splicing was found to be predominantly driven by cis- regulatory changes. However, trans changes affecting splicing make be central to plasticity as they were impacted more by environmental variation. Finally, we performed scans for selection and found that, while genes with splicing divergence more often co-localized with genomic outliers associated with metabolic traits, they were not enriched for genomic outliers. Overall, our results provide evidence that alternative splicing plays an important role in gene regulation in house mice, contributing to adaptation and plasticity.

evolutionary biology↗

bioRxiv2024

Gene-by-environment interactions and adaptive body size variation in mice from the Americas

The relationship between genotype and phenotype is often mediated by the environment. Moreover, gene-by-environment (GxE) interactions can contribute to variation in phenotypes and, in turn, fitness. Nevertheless, understanding the impact of GxE interactions in wild systems remains challenging. In the last 500 years, house mice have invaded the Americas. Despite their short residence time, there is evidence of rapid climate adaptation, including shifts in body size and aspects of metabolism with latitude. Previous studies in this system have identified candidate genes for metabolic adaptation using selection scans, however, environmental variation in diet as well as GxE interactions affecting metabolism are likely important factors in shaping body mass variation in wild populations. Here, we investigate the role of the environment and GxE interactions in shaping adaptive phenotypic variation with an experimental manipulation of diet. Using new locally adapted inbred strains from North and South America, we evaluated response to a high-fat diet, finding that sex, strain, diet, and the interaction between strain and diet contribute significantly to variation in aspects of body size. We also found that transcriptional response to diet is largely strain-specific, indicating that GxE interactions affecting gene expression are pervasive. Next, we used crosses between strains from contrasting climates (New York x Brazil and New York x Florida) to characterize gene expression regulatory divergence on a standard breeder diet and on a high-fat diet. We found that gene regulatory divergence is often condition-specific, particularly for trans-acting changes. Finally, we find evidence for lineage-specific selection on cis-regulatory variation involved in diverse processes, including lipid metabolism. Overlap with scans for selection identified candidate genes for environmental adaptation with diet-specific effects. Together, our results underscore the importance of environmental variation and GxE interactions to adaptive variation in complex traits.

evolutionary biology↗

bioRxiv2023

Across two continents: the genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas

AO_SCPLOWBSTRACTC_SCPLOWParallel clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in regulatory regions. Genes containing the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, and development or function of the eye as well as traits associated with the cardiovascular and renal systems. We then combined these results with published results from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects, providing strong evidence of parallel adaptation and identifying genes that likely underlie recent environmental adaptation in house mice across North and South America. Author summarySince their arrival with European colonizers, house mice have successfully spread throughout the Americas. There is strong evidence that populations in North America have adapted in that time, including parallel evolution of phenotypes across latitude (e.g., body size, behavior) as well as the identification of genes that show signals of selection. Here, we investigate the genetics of environmental adaptation in South America. We find that populations in South America evolve independently of populations in North America. We identify candidate genes for environmental adaptation with links to traits like body size, metabolism, immunity, eye function, and the cardiovascular and renal systems. We then bring together data from three transects across two continents to determine if environmental adaptation is predictable, with parallel genetic changes in response to shared conditions. We find that most evidence of environmental adaptation lies in regulatory regions and that, while most candidate genes are unique to individual transects, many are shared, providing significant evidence of parallel adaptation. We identify a core set of candidate genes independently identified in all three transects that likely contribute to environmental adaptation in the Americas. These results highlight the value of studying wild populations of this genetic model system.

evolutionary biology↗

bioRxiv2023

Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models

The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for a century. However, laboratory mice capture a narrow subset of the genetic variation found in wild mouse populations. This consideration inherently restricts the scope of potential discovery in laboratory models and narrows the pool of potentially identified phenotype-associated variants and pathways. Wild mouse populations are reservoirs of predicted functional and disease-associated alleles, but the sparsity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently imported, sequenced, and phenotyped a set of 11 wild-derived inbred strains developed from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from five environmentally diverse locations across North and South America: Saratoga Springs, New York, USA; Gainesville, Florida, USA; Manaus, Brazil; Tucson, Arizona, USA; and Edmonton, Alberta, Canada. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the mouse reference assembly, with 42.5% of variants in the Nachman strain genomes absent from classical inbred mouse strains. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ.

genetics↗