About

Daniel Rokhsar is a Professor of Physics, Molecular & Cell Biology in the Division of Genetics, Genomics, Evolution, and Development at the University of California, Berkeley. His research focuses on advances at the interface between genetics, genomics, and computational biology, encompassing both applications and methodological development. His areas of interest include new model organism genome assembly and annotation for both plants and animals, the development of novel computational methods for analyzing sequencing data, and evolutionary genomics.

Research topics

• Biology
• Agronomy
• Biotechnology
• Botany
• Genetics

Selected publications

• Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches

  Nature Ecology & Evolution · 2026-03-30

  articleOpen accessSenior author

  The evolutionary relationships among decapodiform lineages (cuttlefish and diverse types of squid) remain uncertain, with implications for the origin of internalized structures (for example, gladius, cuttlebone and coiled shell) derived from the ancestral chambered shell as well as the ecological shifts between the deep ocean and shallow coastal habitats. To address these questions, we adopted a phylogenomic approach that integrated three new high-quality genome sequences with available genomic and transcriptomic datasets. Our analyses support a novel topology that separates a clade of open-ocean lineages (Oegopsida and Spirulida, together Acorneata) from a clade comprising the remaining coastal and shallow-water orders (Sepiida, Myopsida, Idiosepiida and Sepiolida, together Corneata). Molecular clock estimates suggest a rapid cladogenesis of modern decapodiform orders in the deep open ocean during the mid-Cretaceous, consistent with fossil data. This early diversification set a 'long fuse' that led to the explosive radiation of squid and cuttlefish into coastal and shallow-water environments as they recovered from the Cretaceous-Palaeogene extinction event.

  PublisherOA PDFDOI

• Priapulids polarise the recurrent genomic evolution of Ecdysozoa

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-01

  datasetOpen access
  PublisherDOI

• Priapulids polarise the recurrent genomic evolution of Ecdysozoa

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-01

  datasetOpen access
  PublisherDOI

• Population Genomics Reveals Local Adaptation Related to Temperature Variation in Two Stream Frog Species: Implications for Vulnerability to Climate Warming

  Molecular Ecology · 2025-01-17 · 5 citations

  article

  Identifying populations at highest risk from climate change is a critical component of conservation efforts. However, vulnerability assessments are usually applied at the species level, even though intraspecific variation in exposure, sensitivity and adaptive capacity play a crucial role in determining vulnerability. Genomic data can inform intraspecific vulnerability by identifying signatures of local adaptation that reflect population-level variation in sensitivity and adaptive capacity. Here, we address the question of local adaptation to temperature and the genetic basis of thermal tolerance in two stream frogs (Ascaphus truei and A. montanus). Building on previous physiological and temperature data, we used whole-genome resequencing of tadpoles from four sites spanning temperature gradients in each species to test for signatures of local adaptation. To support these analyses, we developed the first annotated reference genome for A. truei. We then expanded the geographic scope of our analysis using targeted capture at an additional 11 sites per species. We found evidence of local adaptation to temperature based on physiological and genomic data in A. montanus and genomic data in A. truei, suggesting similar levels of sensitivity (i.e., susceptibility) among populations regardless of stream temperature. However, invariant thermal tolerances across temperatures in A. truei suggest that populations occupying warmer streams may be most sensitive. We identified high levels of evolutionary potential in both species based on genomic and physiological data. While further integration of these data is needed to comprehensively evaluate spatial variation in vulnerability, this work illustrates the value of genomics in identifying spatial patterns of climate change vulnerability.

  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 access

  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

• Major cell type differences between larval and adult hemichordate body plans

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-03 · 1 citations

  preprintOpen access

  Abstract A major gap in our understanding of animal development is how adult body plans arise in animals with indirect development, where adults emerge from the transformation of a distinct larval form during metamorphosis. We address this question by examining cellular changes in the enteropneust hemichordate Schizocardium californicum , a species with a complex lifecycle and dramatic metamorphosis. Employing whole-body single-cell RNA sequencing, we chart the cellular composition and transcriptional dynamics of larval, metamorphosis, and adult stages. Our tissue level atlas reveals that ectodermal and endodermal cell types in larvae and adults occupy distinct transcriptional spaces, showing greater similarity to other cell types within the same life stage than to their counterparts in the opposite stage. In contrast, mesodermal cell types from both larvae and adults cluster closely together, indicating conserved transcriptional profiles. These findings demonstrate that the extensive morphological reorganization during metamorphosis is paralleled by profound shifts in cell-type specific transcriptional programs, highlighting the complexity of the larva-to-adult transition.

  PublisherOA PDFDOI

• The genomic origin of the unique chaetognath body plan

  Nature · 2025-08-13 · 11 citations

  articleOpen access

  Abstract The emergence of animal phyla, each with their unique body plan, was a rapid event in the history of animal life, yet its genomic underpinnings are still poorly understood 1 . Here we investigate at the genomic, regulatory and cellular levels, the origin of one of the most distinctive animal phyla, the chaetognaths, whose organismal characteristics have historically complicated their phylogenetic placement 2,3 . We show that these characteristics are reflected at the cell-type level by the expression of genes that originated in the chaetognath lineage, contributing to adaptation to planktonic life at the sensory and structural levels 4 . Similarly to other members of gnathiferans (which also include rotifers and several other microscopic phyla) 5,6 , chaetognaths have undergone accelerated genomic evolution with gene loss and chromosomal fusions 7,8 . Furthermore, they secondarily duplicated thousands of genes 9,10 , without evidence for a whole-genome duplication, yielding, for instance, tandemly expanded Hox genes, as well as many phylum-specific genes. We also detected repeat-rich highly methylated neocentromeres and a simplified DNA methylation toolkit that is involved in mobile element repression rather than transcriptional control. Consistent with fossil evidence 11,12 , our observations suggest that chaetognaths emerged after a phase of morphological simplification through a reinvention of organ systems paralleled by massive genomic reorganization, explaining the uniqueness of their body plan.

  PublisherOA PDFDOI

• A single-cell atlas of the bobtail squid visual and nervous system highlights molecular principles of convergent evolution

  Nature Ecology & Evolution · 2025-06-06 · 12 citations

  articleOpen accessSenior author

  The cephalopod and vertebrate visual systems are a textbook example of convergent evolution with unknown molecular underpinnings. Here we characterize 98,537 single-cell transcriptomes in the bobtail squid Euprymna berryi to understand how the cephalopod retina and optic lobes relate to the vertebrate retina. We confirm the overall relative simplicity of the cephalopod retina but identify two related photoreceptor cell subtypes expressing distinct r-opsins. By contrast, the adult optic lobe contains a diverse repertoire of neuronal and glial cell types, with a predominance of dopaminergic neurons. We show that cephalopod-specific gene duplicates probably contributed to this cell type diversification. Comparing neuronal cell population in the optic lobes of hatchlings and adults, we reveal a switch towards dopaminergic neurotransmitter usage with age, indicative of a maturation process. We further identify an FMRF-amide-based retrograde signal from the optic lobe towards the retina that supports the functional analogy of the cephalopod optic lobe cortex and the vertebrate inner retina in visual signal processing from a molecular standpoint. Finally, comparative analyses with vertebrate and arthropod cells suggest a scenario in which two photoreceptor types and two neuronal populations may have already been present in the eye of the bilaterian ancestor.

  PublisherOA PDFDOI

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

  EvoDevo · 2025-05-31 · 3 citations

  articleOpen access

  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 hagfish genome and the evolution of vertebrates

  Nature · 2024-01-23 · 103 citations

  articleOpen accessSenior authorCorresponding

  Abstract As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution 1–3 . Here we investigate the complex history, timing and functional role of genome-wide duplications 4–7 and programmed DNA elimination 8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami . Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1R V ) that predates the early Cambrian cyclostome–gnathostome split, followed by a mid–late Cambrian allo-tetraploidization (2R JV ) in gnathostomes and a prolonged Cambrian–Ordovician hexaploidization (2R CY ) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan 1,2 . Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys 10,11 . Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates.

  PublisherDOI

Recent grants

• NIH Grant R01GM086321

  NIH · $2.5M · 2017

• NIH Grant R01HD065705

  NIH · $1.2M · 2015

• Berkeley Training Program in Genomics and Computational Biology

  NIH · $12.6M · 2000–2030

• NIH Grant S10OD018174

  NIH · $600k · 2015

• BREAD ABRDC: Development of Genomic Resources in Water Yam (Dioscorea alata L.) for Accelerated Breeding and Improvement

  NSF · $1.5M · 2016–2022

Frequent coauthors

• Jeremy Schmutz

  HudsonAlpha Institute for Biotechnology

  265 shared

• Jane Grimwood

  HudsonAlpha Institute for Biotechnology

  243 shared

• Erika Lindquist

  Lawrence Berkeley National Laboratory

  179 shared

• Igor V. Grigoriev

  Lawrence Berkeley National Laboratory

  160 shared

• Astrid Terry

  Wellcome Centre for Molecular Parasitology

  154 shared

• Simon Prochnik

  Lawrence Berkeley National Laboratory

  154 shared

• Jarrod Chapman

  Joint Genome Institute

  149 shared

• Asaf Salamov

  Joint Genome Institute

  146 shared

Education

• Ph.D., Physics

  Cornell University

  1987

• M.S., Physics

  Cornell University

  1985

• A.B., Physics

  Princeton University

  1982