About

Christopher Lowe is the John B. and Jean De Nault Professor of Marine Science at the Hopkins Marine Station within the Department of Biology at Stanford University. He trained as a biologist in the UK at Sussex University, earning a BSc. Hons in Biology with European Studies in 1991. He completed his PhD in Ecology and Evolution at SUNY Stony Brook in 1998, where he worked on the evolution of body plans and the origin of echinoderms. Following his doctoral studies, he was a Miller Fellow at UC Berkeley, focusing on the origin of chordates and the evolution of the vertebrate central nervous system, working with prominent researchers including Mike Levine, John Gerhart, and Marc Kirschner. His academic career began as an Assistant Professor at the University of Chicago in 2005, and he moved to Stanford in 2010, where his lab is based at Hopkins Marine Station in Monterey. His primary research interests involve understanding how major groups of animals evolved, with a focus on the evolution of deuterostomes, and he is interested in applying emerging biotechnological techniques to new species. His appointment at Hopkins Marine Station provides access to the rich biodiversity of Monterey Bay, supporting his research on marine evolutionary biology.

Research topics

• Biology
• Evolutionary biology
• Anatomy
• Medicine
• Zoology

Selected publications

• Molluscan live-dead mismatch as a gauge of urban footprints and unpolluted baselines in cold waters hostile to shell preservation

  Marine Ecology Progress Series · 2025-04-25

  articleOpen access

  Assessing the health of benthic ecosystems is crucial for understanding anthropogenic impacts and guiding remediation efforts, but conventional methods relying upon a one-time sampling face many challenges in estimating the pre-impact state and identifying unaffected areas. Here, we used species-level abundance data for living and dead mollusks acquired from a single sampling (2014) of the monitoring grid for the Macaulay Point outfall (City of Victoria, British Columbia, Canada), which discharged untreated municipal wastewater into the cold-temperate Juan de Fuca Strait at 60 m water depth from the early 1970s until upgrading to tertiary treatment in 2020. The footprint of outfall-related nutrients was readily detected: despite corrosive seawater and scant sediment accumulation hostile to shell preservation, molluscan death assemblages retained a sufficient local inventory of shells produced under pre-pollution conditions, which favored suspension feeders, to create a gradient of live-dead mismatch with detritivore-dominated living assemblages. Concerns about postmortem bias against vulnerable shell types were also allayed, as were concerns that strong tidal currents would obscure or obliterate habitat-level differences. Live-dead mismatch was relatively and absolutely small in 2 reference areas, i.e. comparable to the offset expected from under-sampling natural temporal variability in the source living community. These results support using molluscan live-dead analysis to fill pernicious knowledge gaps outside the warm-water settings where the method was developed and to gauge (1) the spatial and ecological footprint of human stressors where data are scarce or suspect, (2) pre-stress baselines within that footprint, and (3) outlying areas that might serve as reference areas for monitoring systems going forward.

  PublisherDOI

• Antero-posterior patterning in the brittle star <i>Amphipholis squamata</i> and the evolution of body plans across echinoderms

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-17 · 3 citations

  preprintOpen accessSenior author

  Abstract Although the adult pentaradial body plan of echinoderms evolved from a bilateral ancestor, identifying axial homologies between the morphologically divergent echinoderms and their bilaterian relatives has been an enduring problem in zoology. The expression of conserved bilaterian patterning genes in echinoderms provides a molecular framework for resolving this puzzle. Recent studies in juvenile asteroids suggest that the bilaterian antero-posterior axis maps onto the medio-lateral axis that is perpendicular to each of the five rays of the pentaradial body plan. Here we test this hypothesis in another echinoderm class, the ophiuroids, using the cosmopolitan brittle star Amphipholis squamata . Our results show that the general principles of axial patterning are similar to those described in asteroids, and comparisons with existing molecular data from other echinoderm taxa support the idea that medio-lateral deployment of the AP patterning program across the rays predates the evolution of the asterozoan and likely the echinoderm crown-groups. Our data also reveal expression differences between A. squamata and asteroids, which we attribute to secondary modifications specific to ophiuroids. Together, this work provides important comparative data to reconstruct the evolution of axial properties in echinoderm body plans.

  PublisherDOI

• Monitoring marine pollution effects through targeted environmental DNA (eDNA) testing in the Pacific northwest

  Marine Pollution Bulletin · 2025-04-27 · 4 citations

  articleOpen access

  Globally, coastal waters experience degradation from pollution associated with multiple discharges, including industrial and agricultural runoff, and municipal wastewater. Certain benthic infaunal taxa are tolerant of high nutrient input and anoxic conditions, while others are sensitive to these conditions. Using these indicator taxa as proxies for assessing organic enrichment is well established to characterize subsequent pollution impacts. Conventional assessment of macroinfauna involves the detailed analysis of each individual specimen within a sample by taxonomic experts, a resource intensive process. As an alternative, we developed sensitive quantitative polymerase chain reaction (qPCR) assays to detect these indicator taxa in a scalable and reliable way. Using whole genome shotgun sequencing, we generated full mitogenome sequences of selected indicator macroinfaunal polychaetes routinely used for monitoring programs in Pacific Northwest marine environments. These sequences were used to design five new, rigorously validated environmental DNA (eDNA) assays capable of detecting low levels of DNA that can be isolated from environmental samples. For nine sites at a wastewater treatment plant outfall in Vancouver, British Columbia, we tested three eDNA sample collection types: active filtration, a passive dip filter from water containing collected macroinfauna, and active filtration from water collected near the sea floor. Generalized linear models indicated that eDNA signal strength correlated with organism count particularly with passive dip sample collection type. eDNA occupancy modelling techniques estimated detection probabilities corresponding with organism count. The present study emphasizes the value of integrating eDNA into marine outfall monitoring efforts to enhance the assessment of environmental effects. • We developed reliable qPCR eDNA assays for selected pollution indicator species. • eDNA assays targeting pollution indicators offer valuable pollution monitoring data. • We found significant correlation between eDNA signal strength and organism count. • Passive eDNA samplers are simple to integrate into conventional monitoring. • eDNA occupancy modelling provides detection probabilities useful for decision-makers.

  PublisherDOI

• Antero-posterior patterning in the brittle star Amphipholis squamata and the evolution of echinoderm body plans

  EvoDevo · 2025-05-31 · 3 citations

  articleOpen accessSenior author

  Although the adult pentaradial body plan of echinoderms evolved from a bilateral ancestor, identifying axial homologies between the morphologically divergent echinoderms and their bilaterian relatives has been an enduring problem in zoology. The expression of conserved bilaterian patterning genes in echinoderms provides a molecular framework for resolving this puzzle. Recent studies in juvenile asteroids suggest that the bilaterian antero-posterior axis maps onto the medio-lateral axis of the arms, perpendicular to the proximo-distal axis of each of the five rays of the pentaradial body plan. Here, we test this hypothesis in another echinoderm class, the ophiuroids, using the cosmopolitan brittle star Amphipholis squamata. Our results show that the general principles of axial patterning are similar to those described in asteroids, and comparisons with existing molecular data from other echinoderm taxa support the idea that medio-lateral deployment of the bilaterian AP patterning program across the rays predates the evolution of the asterozoans, and likely the echinoderm crown-group. Our data also reveal expression differences between A. squamata and asteroids, which we attribute to secondary modifications specific to ophiuroids. Together, this work provides important comparative data to reconstruct the evolution of axial properties in echinoderm body plans.

  PublisherOA PDFDOI

• The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution

  Nature · 2025-09-24 · 6 citations

  review
  PublisherDOI

• Two parallel lineage-committed progenitors contribute to the developing brain

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-03 · 1 citations

  preprintOpen access

  Abstract The hindbrain is a life-sustaining brain region. In one model, a common neural progenitor generates all brain regions. Here our studies of mouse embryos and human pluripotent stem cells (hPSCs) support a different model: two parallel brain progenitors emerge simultaneously during gastrulation, anterior neural ectoderm (forebrain/midbrain progenitor) and posterior neural ectoderm (hindbrain progenitor). Not only are they lineage-committed to respectively form forebrain/midbrain vs. hindbrain in vitro , but they also have diverging chromatin landscapes foreshadowing future forebrain/midbrain vs. hindbrain identities. Leveraging these differences, we differentiated hPSCs into hindbrain rhombomere 5/6-specific motor neurons, hitherto difficult to generate in vitro . We postulate the brain is a composite organ emanating from two lineage-restricted progenitors; these dual progenitors may be evolutionarily conserved across 550 million years from hemichordates to mammals.

  PublisherOA PDFDOI

• See-Star: a versatile hydrogel-based protocol for clearing large, opaque and calcified marine invertebrates

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-17

  preprintOpen accessSenior author

  Abstract Studies of morphology and developmental patterning in adult stages of many invertebrates are hindered by opaque structures, such as shells, skeletal elements, and pigment granules that block or refract light and necessitate sectioning for observation of internal features. An inherent challenge in studies relying on surgical approaches is that cutting tissue is semi-destructive, and delicate structures, such as axonal processes within neural networks, are computationally challenging to reconstruct once disrupted. To address this problem, we developed See-Star, a hydrogel-based tissue clearing protocol to render the bodies of opaque and calcified invertebrates optically transparent while preserving their anatomy in an unperturbed state, facilitating molecular labeling and observation of intact organ systems. The resulting protocol can clear large (&gt;1 cm 3 ) specimens to enable deep-tissue imaging, and is compatible with molecular techniques, such as immunohistochemistry and in situ hybridization to visualize protein and mRNA localization. To test the utility of this method, we performed a whole mount imaging study of intact nervous systems in juvenile echinoderms and molluscs, and demonstrate that See-Star allows for comparative studies to be extended far into development facilitating insights into the anatomy of juveniles and adults that are usually not amenable to whole mount imaging.

  PublisherOA PDFDOI

• Pluripotency of a founding field: rebranding developmental biology

  Development · 2024-02-01 · 6 citations

  articleOpen access

  The field of developmental biology has declined in prominence in recent decades, with off-shoots from the field becoming more fashionable and highly funded. This has created inequity in discovery and opportunity, partly due to the perception that the field is antiquated or not cutting edge. A 'think tank' of scientists from multiple developmental biology-related disciplines came together to define specific challenges in the field that may have inhibited innovation, and to provide tangible solutions to some of the issues facing developmental biology. The community suggestions include a call to the community to help 'rebrand' the field, alongside proposals for additional funding apparatuses, frameworks for interdisciplinary innovative collaborations, pedagogical access, improved science communication, increased diversity and inclusion, and equity of resources to provide maximal impact to the community.

  PublisherOA PDFDOI

• Shifting Epidemiology of Carbapenemase-Producing Organisms: Time Series Analysis of the Provincial Surveillance Program in British Columbia, Canada from 2014-2023

  SSRN Electronic Journal · 2024-01-01

  preprintOpen access
  PublisherDOI

• Algorithmic construction of topologically complex biomineral lattices via cellular syncytia

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-21 · 1 citations

  preprintOpen access

  Abstract Biomineralization is ubiquitous in both unicellular and multicellular living systems [1, 2] and has remained elusive due to a limited understanding of physicochemical and biomolecular processes [3]. Echinoderms, identified with diverse architectures of calcite-based structures in the dermis[4], present an enigma of how cellular processes control shape and form of individual structures. Specifically, in holothurians (sea cucumbers), multi-cellular clusters construct discrete single-crystal calcite ‘ossicles’ ( ∼ 100 µ m length scale), with diverse morphologies both across species and even within an individual animal [5]. The local rules that might encode these unique morphologies in calcite ossicles in holothurians remain largely unknown. Here we show how transport processes in a cellular syncytium impart a top-down control on ossicle geometry via symmetry breaking, branching, and fusion in finite cellular clusters. As a unique example of cellular masonary, we show how coordination within a small cluster of cells builds calcite structures about an order of magnitude larger than any individual participating cell. We establish live imaging of ossicle growth in Apostichopus parvimensis juveniles revealing how individual crystalline seeds ( ∼ 1 − 2 µ m) grow inside a multi-cellular syncytial complex with the biomineral completely wrapped within a membrane-bound cytoplasmic sheath. Constructing a topological description of ossicle geometries from 3D micro-CT (computational tomography) data reveals the hidden growth history and conserved patterns across ossicle types. We further demonstrate vesicle transport on the surface of the ossicle, rather than cell motility, regulates material transport to the ossicle tips via a unique cytoskeletal architecture. Finally, using reduced order models of conserved transport on self-closing active branching networks, we highlight the hidden universality in the growth process of distinct ossicles. The system presented here serves as a unique playground merging top-down cellular physiology and classical branching morphogenesis [6] with bottom-up non-equilibrium mineralization [7] processes at the interface of living and non-living matter [8].

  PublisherOA PDFDOI

Recent grants

• Deuterostome Endomesoderm Specification: Insights from Hemichordates

  NSF · $338k · 2010–2013

• Collaborative Research: Turbulence-spurred settlement: Deciphering a newly recognized class of larval response

  NSF · $260k · 2014–2018

• The Evolution of Retinoid Signaling in Deuterostomes: Insights from Hemichordates

  NSF · $500k · 2013–2016

• Hemichordate neural organization: generating neural system diversity from conserved molecular patterning

  NSF · $726k · 2018–2022

Frequent coauthors

• Laurent Formery

  Pacific University

  68 shared

• Daniel S. Rokhsar

  Innovative Genomics Institute

  45 shared

• John C. Gerhart

  University of California, Berkeley

  41 shared

• Muriel H. Walker

  37 shared

• Ariel M. Pani

  University of Virginia

  37 shared

• Mark Q. Martindale

  Whitney Museum of American Art

  36 shared

• Billie J. Swalla

  University of Washington

  33 shared

• John F. Fallon

  31 shared

Labs

• Lowe LabPI

Education

• PhD, Ecology and Evolution

  Stony Brook University

  1998

• BSc. Hons, Biology

  University of Sussex

  1991