About

Interdisciplinary Research Spanning Physical Process and Biological Evolution at Ecologic and Geologic Timescales. Evolution & Development, Early Animal Evolution, Evolution of Complex Multicellularity, Sense Organ Evolution In Basal Animal, Paleobiology, Multicellularity and Neo-Proterozoic/Cambrian Radiation, Climatic and Oceanic Controls on Fossil and Modern Diversity, Fossil Cephalopod Form & Function, Tectonic and Faunal Evolution of the Sea of Cortez, Historical Ecology, Coastal Process & Conservation Genetics, Landscape Evolution of Polynesian Coasts, Geomorphology, History, Ecology and Restoration of California Lagoons & Estuaries, Conservation Genetics, Speciation & Biodiversity of Estuarine Taxa

Research topics

• Ecology
• Biology
• Geography
• Biochemistry
• Paleontology
• Evolutionary biology
• Fishery

Selected publications

• A chromosome-level genome assembly for the beach-spawning California grunion, <i>Leuresthes tenuis</i>

  Journal of Heredity · 2026-01-31

  articleOpen accessSenior author

  We generated the first chromosome-level genome assembly for California grunion, Leuresthes tenuis, using PacBio HiFi long reads and Omni-C chromatin-proximity sequencing, yielding a 0.917 Gb genome with a scaffold N50 of 35 Mb and a BUSCO completeness score of 99.37. This beach-spawning marine silverside is the target of a unique recreational hand-grab fishery during its nocturnal spawning runs. Regulation of this fishery, initiated in 1927, remained unchanged from 1949 to 2022, when recent data suggesting a stock decrease led California Department of Fish and Wildlife to reduce the fishing season length. California grunion are endemic to the coast of California and northern Baja California, but within the last two decades the northern limit of spawning has expanded roughly 470 kilometers from Point Conception to north of San Francisco Bay. This genome will facilitate studies addressing the temporal and spatial genetic stock structure, and recent range expansion, of this unique charismatic native species and will also allow assessment of genetic responses to present and future environmental challenges such as changing temperature, and pollution as well as the impacts of harvest and effects of management.

  PublisherDOI

• Efficacy of environmental DNA metabarcoding in monitoring fish faunas in California estuaries and lagoons: a preliminary assessment

  Research Square · 2025-07-07

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Reference genome for the endangered, genetically subdivided, northern tidewater goby, <i>Eucyclogobius newberryi</i>

  Journal of Heredity · 2024-10-05 · 2 citations

  articleOpen access1st authorCorresponding

  The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby, NTG) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980 Mb E. newberryi reference genome has an N50 of 34 Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the NTG, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.

  PublisherOA PDFDOI

• Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

  Peer Community Journal · 2023-04-06 · 3 citations

  articleOpen accessSenior author

  Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had different effects on community composition for each primer, especially for the 16S, when using a filter of larger pore size (3 μm). Nevertheless, pre-freezing water samples can still be a viable alternative for storage and processing of turbid water samples when focusing on fish communities (12S). The use of sediment samples as an alternative to processing water samples should be done with caution, and at minimum the number of biological replicates and/or volume sampled should be increased.

  PublisherOA PDFDOI

• The passing of Edgar Samuel

  Jewish historical studies · 2023-05-19

  articleOpen access1st authorCorresponding

  Edgar about his father, he says of him that he acquired a professional standard of expertise as a researcher and writer, and made a significant contribution to the history of the Jewish community in England. Wilfred was the main founder of the Jewish Museum in London,

  PublisherOA PDFDOI

• A Broad Survey of Gene Body and Repeat Methylation in Cnidaria Reveals a Complex Evolutionary History

  Genome Biology and Evolution · 2022-01-27 · 11 citations

  articleOpen accessSenior authorCorresponding

  DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.

  PublisherOA PDFDOI

• Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-06-20 · 2 citations

  preprintOpen accessSenior author

  Abstract Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had different effects on community composition for each primer, especially for the 16S, when using a filter of larger pore size (3 μm). Nevertheless, pre-freezing water samples can still be a viable alternative for storage and processing of turbid water samples when focusing on fish communities (12S). The use of sediment samples as an alternative to processing water samples should be done with caution, and at minimum the number of biological replicates and/or volume sampled should be increased.

  PublisherOA PDFDOI

• Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach

  Molecular Ecology · 2022-10-07 · 4 citations

  articleOpen accessSenior author

  Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current "management-by-phenotype" approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.

  PublisherOA PDFDOI

• Causes and consequences of the late Holocene extinction of the marine flightless duck (Chendytes lawi) in the northeastern Pacific

  Quaternary Science Reviews · 2021 · 31 citations

  • Ecology
  • Biology
  • Fishery

  The extinction of California’s flightless duck, Chendytes lawi, stands out in the faunal history of North America because it involved a marine animal that disappeared in the late Holocene, not in the terminal Pleistocene when humans arrived from Asia, nor with the more recent entry of Europeans and associated resource exploitation. Here we evaluate the duck’s ecology by combining a stable isotopic evaluation of its feeding niche with records of human predation and climatic variation to evaluate (1) alternative influences on the duck’s extinction and (2) possible ecological consequences of its disappearance. Results indicate that a mid-late Holocene increase in human population density coincided with a decrease in mean sea surface temperatures (SST) and an increase in SST variance, all of which were contemporaneous with the demise of the flightless duck ca. 2500 cal BP. Climate appears to be a main exogenous driver of this extinction event by not only negatively impacting flightless duck food availability, but positively impacting one of the duck’s main predators: humans. Isotopic findings indicate the duck had a unique feeding ecology that overlapped equally with analog species reliant mostly on marine invertebrates (sea otters [Enhydra lutris]) and on fish (harbor seals [Phoca vitulina]). This dietary niche overlap suggests the duck’s extinction could have opened foraging opportunities for harbor seals and sea otters. Otter numbers appear to have increased coincident with the duck’s decline which also correlates with a decrease in size and abundance of red abalone (Haliotis rufescens), one of the otter’s preferred prey. These correlations suggest that new feeding opportunities may have emerged for otters in the face of the duck’s extinction, encouraging an increase in otter populations, which then had negative impacts on abalone that also were targeted by humans. Overall findings suggest the possibility of an unanticipated prehistoric precursor to the historic baseline of this nearshore ecosystem.

  PublisherDOI

• Fossil Corals With Various Degrees of Preservation Can Retain Information About Biomineralization-Related Organic Material

  Frontiers in Earth Science · 2021-06-23 · 9 citations

  articleOpen accessSenior authorCorresponding

  Scleractinian corals typically form a robust calcium carbonate skeleton beneath their living tissue. This skeleton, through its trace element composition and isotope ratios, may record environmental conditions of water surrounding the coral animal. While bulk unrecrystallized aragonite coral skeletons can be used to reconstruct past ocean conditions, corals that have undergone significant diagenesis have altered geochemical signatures and are typically assumed to retain insufficient meaningful information for bulk or macrostructural analysis. However, partially recrystallized skeletons may retain organic molecular components of the skeletal organic matrix (SOM), which is secreted by the animal and directs aspects of the biomineralization process. Some SOM proteins can be retained in fossil corals and can potentially provide past oceanographic, ecological, and indirect genetic information. Here, we describe a dataset of scleractinian coral skeletons, aged from modern to Cretaceous plus a Carboniferous rugosan, characterized for their crystallography, trace element composition, and amino acid compositions. We show that some specimens that are partially recrystallized to calcite yield potentially useful biochemical information whereas complete recrystalization or silicification leads to significant alteration or loss of the SOM fraction. Our analysis is informative to biochemical-paleoceanographers as it suggests that previously discounted partially recrystallized coral skeletons may indeed still be useful at the microstructural level.

  PublisherOA PDFDOI

Recent grants

• DISSERTATION RESEARCH: An interdisciplinary approach to testing intraspecific evolutionary processes

  NSF · $15k · 2011–2014

Frequent coauthors

• Arnold I. Miller

  University of Cincinnati

  27 shared

• J. John Sepkoski

  25 shared

• M. G. Sommers

  National Center for Ecological Analysis and Synthesis

  25 shared

• Kaustuv Roy

  25 shared

• Karen M. Bezusko

  University of Cincinnati

  25 shared

• David M. Raup

  University of Chicago

  25 shared

• Philip M. Novack‐Gottshall

  Benedictine University

  25 shared

• John Alroy

  Macquarie University

  25 shared

Labs

• Jacobs Lab at UCLAPI

  Principal Investigator Dr. David K. Jacobs

Education

• BA

  Cornell University

• MS

  University of Chicago

• PhD

  Virginia Polytechnic Institute