About

Michael Nachman is a Professor of Integrative Biology at the University of California, Berkeley, with research interests spanning evolutionary biology and phylogenetics, gene expression and regulation, genomics and genetics, and population genetics. His lab studies population, evolutionary, and ecological genetics and genomics, focusing on understanding how genetic variation in natural populations is shaped by the interplay of migration, mutation, selection, recombination, drift, and changes in population size. The research addresses fundamental questions in population genetics and genomics, including the genetic mechanisms underlying the formation of new species and the genetics of adaptation. Most of the work is conducted on mammals, with a particular emphasis on humans and mice.

Research topics

• Social Science
• Biology
• Ecology
• Computer Science
• Sociology
• Zoology
• Genetics
• Evolutionary biology
• Engineering ethics
• Paleontology
• Data science
• Immunology
• Engineering

Selected publications

• Author response: Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils

  2025-09-12

  peer-reviewOpen access
  PublisherDOI

• A highly contiguous genome assembly for the wrentit ( <i>Chamaea fasciata</i> ), the sole representative of the babbler radiation in the Americas

  Journal of Heredity · 2025-09-04

  articleOpen access

  The wrentit (Chamaea fasciata) is a chaparral and scrub specialist bird found from coastal Oregon to northern Baja California. We generated a draft reference assembly for the species using PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project. Sequenced reads were assembled into 1342 scaffolds totaling 1.19 gigabase in length. A contig N50 of 4.5 Mb, scaffold N50 of 73.3 Mb, and Benchmarking Universal Single-Copy Orthologs completeness score of 96.8% indicate that the wrentit genome is a highly contiguous assembly in line with other high quality avian assemblies. An annotation of the assembly identified 16 821 protein-coding genes. We detected a translocation between chromosome 4A of the zebra finch to the Z chromosome of the wrentit. This translocation has previously been identified as a neo-sex chromosome shared across the superfamily Sylvioidea. Finally, we found a negative correlation between transposable element richness and gene density across the genome, but a positive relationship between guanine-cytosine content and gene density. This reference will serve as an essential resource for studies on the biogeography, local adaptation, and conservation genetics of this iconic species of California's chaparral.

  PublisherOA PDFDOI

• Species boundaries, hybridization and gene flow

  Therya · 2025-01-31

  articleOpen access1st authorCorresponding

  The rise of genomics has spurred a renewed interest in hybridization and the permeability of species boundaries. However, these ideas are not new. Here I review early work by Patton and colleagues on hybridization, gene flow, and the nature of species boundaries in pocket gophers and argue that a focus on the underlying biology of the organism provides insights into hybridization and gene flow that are not obtainable from genomic data alone.

  PublisherDOI

• Genetic structure and demographic history of house mice in western Europe inferred using whole-genome sequences

  Proceedings of the Royal Society B Biological Sciences · 2025-04-01

  articleOpen accessSenior author

  The western house mouse, Mus musculus domesticus , is a human commensal and an outstanding model organism for studying a wide variety of traits and diseases. However, we have few genomic resources for wild mice and only a rudimentary understanding of the demographic history of house mice in Europe. Here, we sequenced 59 whole genomes of mice collected from England, Scotland, Wales, Guernsey, northern France, Italy, Portugal and Spain. We combined this dataset with 24 previously published sequences from southern France, Germany and Iran and compared patterns of population structure and inferred demographic parameters for house mice in western Europe to patterns seen in humans. Principal component and phylogenetic analyses identified three genetic clusters in western European mice. Admixture and f -branch statistics identified historical gene flow between these genetic clusters. Demographic analyses suggest a shared history of population bottlenecks prior to 20 000 years ago. Estimated divergence times between populations of house mice from western Europe ranged from 1500 to 5500 years ago, in general agreement with the zooarchaeological record. These results correspond well with key aspects of contemporary human population structure and the history of migration in western Europe, highlighting the commensal relationship of this important genetic model.

  PublisherDOI

• Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils

  eLife · 2025-09-12 · 1 citations

  articleOpen access

  Tuberculosis is a heterogeneous disease in humans with individuals exhibiting a wide range of susceptibility. This heterogeneity is not captured by standard laboratory mouse lines. We used a new collection of 19 wild-derived inbred mouse lines collected from diverse geographic sites to identify novel phenotypes during Mycobacterium tuberculosis ( Mtb ) infection. Wild-derived mice have heterogeneous immune responses to infection that result in differential ability to control disease at early time points. Correlation analysis with multiple parameters including sex, weight, and cellular immune responses in the lungs revealed that enhanced control of infection is associated with increased numbers of CD4 T cells, CD8 T cells, and B cells. Surprisingly, we did not observe strong correlations between IFN-γ production and control of infection. Although in most lines high neutrophils were associated with susceptibility, we identified a mouse line that harbors high neutrophil numbers yet controls infection. Using single-cell RNA sequencing, we identified a novel neutrophil signature associated with failure to control infection.

  PublisherDOI

• Intraspecific gene regulation in <i>cis-</i> and <i>trans-</i>

  Evolution · 2025-01-27 · 2 citations

  reviewOpen accessSenior author

  Changes in gene expression underlie much of evolution and occur via either cis-acting mutations, which lie near the affected gene and act in a context-specific manner, or trans-acting mutations, which may be far from the affected gene and act through diffusible molecules such as transcription factors. A commonly held view is that most expression variation within species is controlled in trans- while expression differences between species are largely controlled in cis-. Here, we summarize recent intraspecific gene regulation studies and find, contrary to this widely held view, that many studies in diverse taxa have revealed a large role for cis-acting mutations underlying expression variation within species. A review of the existing literature also shows that preparations using whole organisms rather than individual tissues may be biased toward identifying trans-regulation. Moreover, we note several examples of predominantly cis-acting regulation in recently diverged populations adapted to different environments. We highlight the challenges of drawing general conclusions from comparisons among studies that use different methodologies and we offer suggestions for studies that will address outstanding questions concerning the evolution of gene regulation.

  PublisherOA PDFDOI

• Patterns of Genetic Diversity Within Three California Quail Species Are Best Explained by Climate and Landscape Changes

  Molecular Ecology · 2025-09-08 · 1 citations

  article

  Many North American game animals experienced severe population declines during the 19th century due to market hunting. However, estimates of the timing and magnitude of these declines often rely on anecdotal evidence, which makes it difficult to understand the lasting impacts of hunting pressures versus climate or landscape changes on the genetic diversity of contemporary populations. Historical reports suggest the California quail (Callipepla californica) suffered more significant hunting pressure in the late 19th century relative to either Gambel's (Callipepla gambelii) or mountain quail (Oreortyx pictus). Genomic data can help illuminate the extent to which historical exploitation moulded the genetic health of modern quail populations. We compared whole genome sequences from these three quail species to evaluate whether reported differences in hunting pressure affected contemporary patterns of genetic diversity. Contrary to our expectations, California quail did not exhibit any evidence for population declines until the late 20th century, long after the era of market hunting ended. California quail also exhibited the highest levels of genetic diversity across most analyses with evidence for population expansion over the past 500,000 years. In contrast, the mountain quail exhibited a long-term population decline beginning in the middle of the last ice age 30-40 thousand years ago. The Gambel's quail appears to have suffered a more recent bottleneck in association with a major drought that impacted the desert southwest during the mid-20th century. Gambel's quail also exhibited increased realised genetic load for mild and moderately deleterious genetic variants. Together, our results demonstrate that market hunting had little lasting impact on the genetic diversity of these quail species, whereas landscape and climate changes have led to fluctuations in effective population size (Ne) and the buildup of genetic load.

  PublisherDOI

• A high-quality genome assembly for a desert-adapted rodent, Merriam’s kangaroo rat (<i>Dipodomys merriami</i>)

  Journal of Heredity · 2025-04-17

  articleOpen accessSenior author

  Merriam's kangaroo rat (Dipodomys merriami) is a member of a unique family of primarily desert-adapted North American rodents (Heteromyidae). Of the 20 species in the genus, D. merriami is one of the most wide-ranging and ecologically flexible, inhabiting desert scrub, grassland, sagebrush steppe, and juniper-piñon woodland in the southwestern deserts of the United States and Mexico. We present a de novo reference genome for D. merriami generated from PacBio HiFi long-read and Omni-C chromatin proximity sequencing as a part of the California Conservation Genomics Project. The primary pseudo-haplotype assembly comprises 3,110 scaffolds, with a contig N50 of 8.6 Mb, scaffold N50 of 49.1 Mb, and a total length of 3.57 Gb. Further, a BUSCO completeness score of 97.8% suggests that the assembly is highly complete. This reference genome will serve as a resource for future studies of Dipodomys conservation genomics, desert adaptation, and phylogeography.

  PublisherOA PDFDOI

• Patterns of genetic diversity within three California quail species are best explained by climate and landscape changes

  2025-04-14

  preprintOpen access

  Many North American game animals experienced severe population declines during the 19th century due to market hunting. However, estimates of the timing and magnitude of these declines often relies on anecdotal evidence, which makes it difficult to understand the lasting impacts of hunting pressures versus climate or landscape changes on the genetic diversity of contemporary populations. Historical reports suggest the California quail (Callipepla californica) suffered more significant hunting pressure in the late 19th century relative to either Gambel’s (Callipepla gambelii) or mountain quail (Oreortyx pictus). Genomic data can help illuminate the extent to which historical exploitation molded the genetic health of modern quail populations. We compared whole genome sequences from these three quail species to evaluate whether reported differences in hunting pressure affected contemporary patterns of genetic diversity. Contrary to our expectations, California quail did not exhibit any evidence for population declines until the late 20th century, long after the era of market hunting ended. California quail also exhibited the highest levels of genetic diversity across most analyses with evidence for population expansion over the past 500,000 years. In contrast, Gambel’s quail appears to have suffered a recent bottleneck in association with a major drought that impacted the desert southwest during the mid-20th century. Gambel’s quail also exhibited increased realized genetic load for mild and moderately deleterious genetic variants. Together, our results demonstrate that market hunting had little lasting impact on the genetic diversity of these quail species, whereas landscape and climate changes have led to fluctuations in effective population size (Ne) and the buildup of genetic load.

  PublisherOA PDFDOI

• A high-quality reference genome for the ornate shrew ( <i>Sorex ornatus</i> )

  Journal of Heredity · 2025-10-03

  articleOpen accessSenior author

  The ornate shrew (Sorex ornatus) is a small predatory mammal with a broad distribution in northern, central, and southern California as well as in Baja California, Mexico. The ornate shrew is a highly productive consumer in wetland environments and is known to hybridize with the closely related vagrant shrew, Sorex vagrans. Here we present a high-quality de novo genome assembly for S. ornatus generated as a part of the California Conservation Genomics Project. The S. ornatus genome was generated using PacBio HiFi long reads and Omni-C chromatin interaction sequencing. The primary assembly is highly contiguous, with a contig N50 of 15.9 Mb, a scaffold N50 of 115.2 Mb, and a BUSCO completeness score of 95.10%. The ornate shrew genome will serve as a valuable resource for future North American Sorex conservation genomics as well as for research into shrew biology more generally.

  PublisherOA PDFDOI

Recent grants

• DISSERTATION RESEARCH: Gene Regulation Evolution and Speciation in House Mice

  NSF · $20k · 2016–2019

• DISSERTATION RESEARCH: Genomic basis of desert adaptation in rodents

  NSF · $20k · 2016–2019

• DISSERTATION RESEARCH: The Genetic Basis of Reproductive Isolation Among Two Species of House Mice

  NSF · $12k · 2006–2008

• Collaborative Research on the Genetic Basis of Reproductive Isolation in House Mice

  NSF · $263k · 2008–2012

• The genomic basis of environmental adaptation in mice

  NIH · $1.3M · 2018–2024

Frequent coauthors

• Katya L. Mack

  54 shared

• Taichi A. Suzuki

  Arizona State University

  52 shared

• Megan Phifer‐Rixey

  Drexel University

  51 shared

• Mallory A. Ballinger

  University of California, Berkeley

  48 shared

• Frédéric Delsuc

  Université de Montpellier

  38 shared

• Christopher A. Emerling

  Reedley College

  37 shared

• Marie‐Ka Tilak

  34 shared

• Rauri C. K. Bowie

  Museum of Vertebrate Zoology

  33 shared

Labs

• Center for Computational BiologyPI