Biology subjects

Kautt, A. F.

Publications and source records attributed to Kautt, A. F..

5 recordsLinked to original sources

bioRxiv2026

Pangenome graphs reveal the extent and complexity of genetic variation in North America's most abundant mammal

Pangenome methods reduce reference bias and enable the characterization of previously inaccessible genomic variation within a species, and are thus especially useful for species with high levels of genetic diversity. Here, we constructed a pangenome for the deer mouse (Peromyscus maniculatus), a model for studying local adaptation and a potent reservoir for diverse zoonotic diseases, using long-read assemblies from 14 ecologically and biogeographically diverse populations and 2 outgroup species (totaling 19 haplotypes). The total length of the pangenome is 3.9 Gb, but only 1.4 Gb is shared across all haplotypes, suggesting vast structural diversity. From this pangenome we identified [~]108.3 million single nucleotide polymorphisms (SNPs), [~]23.9 million indels (variants < 50 bp), and [~]2.4 million structural variants (variants > 50 bp) as well as complex genetic variation driven by massive chromosomal rearrangements and an unprecedented diversity of centromeric satellite positions. Furthermore, we uncover widespread gene copy number variation (CNVs)-some genes vary in number by an order of magnitude across deer mouse haplotypes-in addition to several gene-rich loci that display high levels of structural diversity. Such genes are enriched for functions related to sensory perception, environmental interaction, and immune responses and many display signatures of positive selection at the molecular level, suggesting functional diversification. Our work provides important insight into the utility of pangenomes for genetically diverse species and illuminates underappreciated genomic plasticity within a mammalian species.

evolutionary biology↗

bioRxiv2026

Pleistocene climatic oscillations impact the diversification of deer mice (Peromyscus maniculatus) and the independent evolution of ecotypes

A central question in evolutionary biology is whether local adaptation is predictable when a species repeatedly encounters similar environments. The deer mouse, Peromyscus maniculatus, has a range of over 13 million km2 in North America and may be found in nearly every terrestrial habitat. Because of their abundance and wide habitat preference, deer mice and closely related Peromyscus, which we refer to as the P. maniculatus species complex, are at the forefront of studies of biogeography and local adaptation. Here, we undertake a comprehensive survey of genome-wide and phenotypic diversity to characterize the recent evolutionary history of this group. We sequenced whole genomes from 232 individuals across their range, representing the most thorough genetic sampling of the P. maniculatus species complex to date. We identify six geographically delineated clades, several of which encompass both classically recognized P. maniculatus subspecies as well as other recognized species. Ecological niche modelling suggests that this geographic structure resulted from rapid post-LGM range expansion and adaptation to emerging habitats. Our morphological measurements of 979 specimens and field data compiled from over 28,000 museum records show that deer mice in forests across the range consistently have longer tails, larger feet, bigger ears, and elongated whiskers. These traits constitute an arboreal ecotype that has evolved at least three times independently, and was likely lost in other parts of the range as populations moved out of forested habitat. Altogether, these results suggest that post-LGM increases in forested habitat drove the parallel evolution of arboreal ecotypes across the deer mouse range.

evolutionary biology↗

bioRxiv2025

The Functional and Genetic Architecture of Olfaction in Deer Mice

Mammals have well-developed olfactory systems, but the molecular logic driving the extraction of biological information, how this logic evolves and contributes to differences in behavior remain unclear. To address this, we generated a chromosome-level assembly of the North American deer mouse, Peromyscus maniculatus, meticulously annotating the complex olfactory subgenome. Comparative analysis revealed high evolutionary plasticity within chemosensory gene families. Rodent olfactory and vomeronasal sensory pathways, predominantly associated with odor learning and innate responses, respectively, show divergent evolutionary trajectories-one conserved, the other rapidly evolving. Despite overall vomeronasal gene dynamism, we identified receptors conserved across evolutionary timescales. Using the activation of these receptors as readouts, we demonstrate the conservation of receptor-ligand pairings for subsets of vomeronasal sensory neurons. Collectively, our findings provide insights into the evolution of the mammalian olfactory systems, highlighting key differences in receptor repertoires and establishing deer mice as a model clade to investigate neural mechanisms underlying the evolution of olfactory pathways and their impact on behavioral evolution. TeaserThe deer mouse genome analysis reveals conserved and divergent components of the rodent olfactory subgenome.

evolutionary biology↗

bioRxiv2021

A novel enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice

Identifying the genetic basis of repeatedly evolved traits provides a way to reconstruct their evolutionary history and ultimately investigate the predictability of evolution. Here, we focus on the oldfield mouse (Peromyscus polionotus), which occurs in the southeastern United States, where it exhibits considerable coat-color variation. Dorsal coats range from dark brown in mice inhabiting mainland habitat to near white on the white-sand beaches of the southeastern US, where light pelage has evolved independently on Floridas Gulf and Atlantic coasts as an adaptation to visually hunting predators. To facilitate genomic analyses in this species, we first generated a high-quality, chromosome-level genome assembly of P. polionotus subgriseus. Next, in a uniquely variable mainland population that occurs near beach habitat (P. p. albifrons), we scored 23 pigment traits and performed targeted resequencing in 168 mice. We find that variation in pigmentation is strongly associated with a ~2 kb region approximately 5 kb upstream of the Agouti-signaling protein (ASIP) coding region. Using a reporter-gene assay, we demonstrate that this regulatory region contains an enhancer that drives expression in the dermis of mouse embryos during the establishment of pigment prepatterns. Moreover, extended tracts of homozygosity in this region of Agouti indicate that the light allele has experienced recent and strong positive selection. Notably, this same light allele appears fixed in both Gulf and Atlantic coast beach mice, despite these populations being separated by >1,000km. Given the evolutionary history of this species, our results suggest that this newly identified Agouti enhancer allele has been maintained in mainland populations as standing genetic variation and from there has spread to, and been selected in, two independent beach mouse lineages, thereby facilitating their rapid and parallel evolution.

evolutionary biology↗

bioRxiv2020

Towards complete and error-free genome assemblies of all vertebrate species

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

genomics↗