About

Professor Elliot Anderson is the inaugural director of the new AI lab for the Arts Division at UC Santa Cruz and serves as the chair of the Art Department. His background combines extensive experience in bridging art and technology, with a focus on exploring the intersection of creative practice and technological innovation. Anderson's work emphasizes the importance of play and exploration in art, fostering opportunities for faculty and students to engage with advanced technologies in an equitable manner, especially supporting underrepresented and first-generation students. His academic journey began with a focus on computer science, earning a B.A. in computer engineering from Northeastern after initially studying architecture at Boston Architectural College. During the 1980s, he worked on flight simulators and interactive computer graphics, which he considers an art practice. Seeking greater artistic freedom, Anderson completed an interdisciplinary Master’s degree in art and philosophy at San Francisco State University, during which he also began teaching. His artistic practice includes projects like a 2007 solo exhibition at the de Young Museum, where he recreated a 19th-century American landscape painting through programming, software, and tourist photos, resulting in large-scale lightbox displays. At UC Santa Cruz since the late 1990s, Anderson has contributed to integrating arts and technology through initiatives such as animation classes and the development of programs like Creative Technologies. His leadership in establishing the A4 AI lab, supported by a donation from AMD, aims to foster faculty research, student engagement, and stronger connections to Silicon Valley’s technological ecosystem. Anderson emphasizes the importance of making arts a participant in technological dialogues and providing students with opportunities to work with cutting-edge tools, internships, and collaborations that prepare them for future innovations in art and technology.

Research topics

• Ecology
• Biology
• Evolutionary biology
• Genetics
• Fishery

Selected publications

• 2026 Genetic referrals

  Open MIND · 2026-01-01

  articleOpen access1st authorCorresponding

  Analytic code for genetic care referral study conducted at MaineHealth

  PublisherOA PDFDOI

• The genetic architecture of ecotypic differentiation in Chinook salmon of the California Central Valley

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-31

  preprintOpen access1st author

  Abstract Understanding the genomic details underlying complex behavioral traits is a foundational pursuit in biology. We use genomic and genetic techniques to dissect the heritable underpinnings of adult migration timing of Chinook salmon in the California Central Valley (CCV), home to several ecotypes not found elsewhere. We find that a previously described genomic region contributes to the seasonal shift in adult freshwater migration in the CCV, as in other river basins, but we further identify two functional domains in this locus that separately and additively influence the trait, with each allele copy affecting timing by ∼two weeks. We show how the evolution of a unique ecotype in the CCV is partially due to an allele derived from the more widespread early-migrating haplotype. However, the genomic background of the evolutionarily differentiated ecotypes contributes a similar amount to trait variation. We show how a relatively simple five-allele genetic system, in concert with genomic backgrounds, can create a remarkable diversity of phenotypes and ecotypes for this iconic species. Teaser A diverse complex of salmon ecotypes is explained by a simple two-locus system and evolutionarily derived genomic backgrounds.

  PublisherOA PDFDOI

• Development of a high-throughput single nucleotide polymorphism panel for genetic stock identification of Striped Bass

  Transactions of the American Fisheries Society · 2025-04-29

  articleOpen access

  ABSTRACT Objective The Striped Bass Morone saxatilis is an anadromous fish that has experienced population declines and recoveries throughout its range from the 1960s to the present day. While many United States fisheries have reopened since the most recent declines, ongoing monitoring is required to ensure that numbers remain stable in the long term. Central to this is the need to determine the extent to which major spawning locations contribute to coastal stocks. While next-generation genomic sequencing can discriminate among closely related breeding aggregations within the Striped Bass native range, the cost per sample of next-generation sequencing methods currently used is too high to be applied to large-scale and long-term projects moving forward. Methods We developed, optimized, and evaluated a GT-Seq panel—a small panel of highly informative single nucleotide polymorphisms—capable of assigning large numbers of Striped Bass to six genetically distinct regions across the Striped Bass spawning range at much lower cost than the previous next-generation sequencing methods. Results The final panel of 233 loci was able to assign 95% of reference individuals to region of origin and had <5% error across all simulations when estimating the mixing proportion of any stock. Conclusions This panel is being used in ongoing characterizations of Striped Bass along the Massachusetts coast and the eastern coast of Nova Scotia. For researchers tracking the migration of Striped Bass throughout their native range, this panel provides a low-cost method of genetically characterizing stocks at specific locations and times that can be easily modified or updated as additional, new genetic data become available.

  PublisherOA PDFDOI

• 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

• <scp>gscramble</scp>: Simulation of Admixed Individuals Without Reuse of Genetic Material

  Molecular Ecology Resources · 2025-01-12

  articleOpen access1st authorCorresponding

  While a best practice for evaluating the behaviour of genetic clustering algorithms on empirical data is to conduct parallel analyses on simulated data, these types of simulation techniques often involve sampling genetic data with replacement. In this paper we demonstrate that sampling with replacement, especially with large marker sets, inflates the perceived statistical power to correctly assign individuals (or the alleles that they carry) back to source populations-a phenomenon we refer to as resampling-induced, spurious power inflation (RISPI). To address this issue, we present gscramble, a simulation approach in R for creating biologically informed individual genotypes from empirical data that: (1) samples alleles from populations without replacement and (2) segregates alleles based on species-specific recombination rates. This framework makes it possible to simulate admixed individuals in a way that respects the physical linkage between markers on the same chromosome and which does not suffer from RISPI. This is achieved in gscramble by allowing users to specify pedigrees of varying complexity in order to simulate admixed genotypes, segregating and tracking haplotype blocks from different source populations through those pedigrees, and then sampling-using a variety of permutation schemes-alleles from empirical data into those haplotype blocks. We demonstrate the functionality of gscramble with both simulated and empirical data sets and highlight additional uses of the package that users may find valuable.

  PublisherDOI

• A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-02

  preprintOpen access1st author

  Abstract Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between individuals within populations have also become common. We present, here, a novel set of multi-allelic microhaplotype genetic markers for Chinook salmon which provide unprecedented resolution for population discrimination and relationship identification from a rapidly and economically assayed panel of markers. We show how this set of microhaplotypes provides definitive power to identify all known lineages of Chinook salmon in California. The inclusion of genetic loci that have known associations with phenotype and that were identified as outliers in examination of whole genome sequence data, allows resolution of stocks that are not highly genetically differentiated but are phenotypically distinct and managed as such. This same set of multiallelic genetic markers have ample variation to accurately identify parent-offspring and full-sibling pairs in all California populations, including the genetically depauperate winter-run lineage. Validation of this marker panel in coastal salmon populations not previously studied with modern genetic methods, also reveals novel biological insights, including the presence of a single copy of a haplotype for a phenotype that has not been documented in that part of the species range, and a clear signal of mixed ancestry for a salmon population that is on the geographic margins of the primary evolutionary lineages present in California.

  PublisherDOI

• Genetic, phenotypic, and environmental drivers of local adaptation and climate change–induced maladaptation in a migratory songbird

  Proceedings of the National Academy of Sciences · 2025-09-29 · 1 citations

  articleOpen access

  Understanding processes driving local adaptation in wild species is a key goal in evolutionary biology, but linking genotype to phenotype to environmental drivers of natural selection remains challenging. Even more rare are empirical examples of what happens when genotype and phenotype fail to keep pace with environmental change. Here, we explore these connections by conducting an integrative study on the breeding range of the yellow warbler ( Setophaga petechia ). Using genome-wide association studies (GWAS), we first identify loci associated with variation in bill morphology and individual quality. We then employ gene–environment association (GEA) analyses and find that precipitation is a key environmental driver of putative selection on bill shape. Finally, we test whether contemporary individuals whose bill shapes deviate from the historical relationship with precipitation experience increased stress (measured by telomere length) as a result of maladaptation. We also use historical DNA to test whether local populations have shifted their ranges over the past century, confirming that the observed changes are not due to range shifts. Our results align with predictions from GWAS and GEA analyses, indicating that birds with shallower bills in increasingly arid regions suffer higher stress (i.e., shorter telomeres) because of maladaptation. Overall, this study links genetic, phenotypic, and environmental data with stress biomarkers to improve understanding of the process of local adaptation and the consequence of failing to keep pace with changing climate conditions.

  PublisherOA PDFDOI

• A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon

  Evolutionary Applications · 2025-05-01 · 5 citations

  articleOpen access1st authorCorresponding

  Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between individuals within populations have also become common. We present here a novel set of multiallelic microhaplotype genetic markers for Chinook salmon, which provide excellent resolution for population discrimination and relationship identification from a rapidly and economically assayed panel of markers. We show how this set of genetic markers assayed by sequencing 204 amplicons, in tandem with a reference dataset of 1636 individual samples from 17 populations, provides definitive power to identify all known lineages of Chinook salmon in California. The inclusion of genetic loci that have known associations with phenotype and that were identified as outliers in examination of whole-genome sequence data allows resolution of stocks that are not highly genetically differentiated but are phenotypically distinct and managed as such. This same set of multiallelic genetic markers has ample variation to accurately identify parent-offspring and full-sibling pairs in all California populations, including the genetically depauperate winter-run lineage. Validation of this marker panel in coastal salmon populations not previously studied with modern genetic methods also reveals novel biological insights, including the presence of a single copy of a haplotype for a phenotype that has not been documented in that part of the species range, and a clear signal of mixed ancestry for a salmon population that is on the geographic margins of the primary evolutionary lineages present in California.

  PublisherOA PDFDOI

• pmparams: an R Package for Defining and Formatting Parameter Tables in Pharmacometric Modeling

  2024-01-01

  articleOpen access
  PublisherDOI

• Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead

  Evolutionary Applications · 2024-03-01 · 5 citations

  articleOpen access

  Abstract Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over 9 years from 2011 to 2019, confidently assigning parentage to 13,576 individuals to determine age and date of spawning and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity among programs. In addition, adaptive genomic variation associated with life history development in this species varied among hatchery programs and was associated with the age of steelhead spawners only in the coastal lineage population. Environmental variation likely contributed to variations in phenotypic patterns observed over time, as our study period spanned both a marine heatwave and a serious drought in California. Our results highlight evidence of a strong genetic component underlying known phenotypic differences in life history traits between two steelhead lineages.

  PublisherOA PDFDOI

Frequent coauthors

• John Carlos Garza

  NOAA National Marine Fisheries Service Southwest Fisheries Science Center

  130 shared

• Kristen Ruegg

  Colorado State University

  99 shared

• Devon E. Pearse

  66 shared

• Thomas B. Smith

  University of California, Los Angeles

  36 shared

• Anthony J. Clemento

  University of California, Santa Cruz

  32 shared

• Robin S. Waples

  University of Washington

  26 shared

• Matthew A. Campbell

  University of California, Davis

  26 shared

• Matthew G. DeSaix

  Animal and Plant Health Inspection Service

  25 shared