About

Joanna L Kelley is a Professor in the Ecology & Evolutionary Biology Department within the Division of Physical & Biological Sciences at the University of California, Santa Cruz. Her research group focuses on evolutionary and functional genomics and adaptation to extreme environments. She is interested in understanding how populations diverge and adapt to the environments they encounter by identifying and characterizing specific genes and pathways that underlie adaptive change. Her approach combines statistical and genomic methods with knowledge from organismal and ecological studies, leveraging natural systems to gain insights into basic biological processes with significant implications for understanding responses to changing environments. Dr. Kelley holds a BA in Mathematics and Biology from Brown University, obtained in 2003, and a PhD in Genome Sciences from the University of Washington, completed in 2008. She completed postdoctoral training in Human Genetics at the University of Chicago from 2008 to 2010 and in Genetics at Stanford University from 2010 to 2013. Her expertise encompasses genomics, evolution, molecular evolution, population biology, genetics, and climate change.

Research topics

• Biology
• Genetics
• Evolutionary biology
• Ecology
• Computational biology
• Computer Science
• Atmospheric sciences
• Physical geography
• Environmental science
• Environmental planning
• Environmental resource management
• Data science
• Oceanography
• Cell biology
• Neuroscience
• Meteorology
• Geology
• Geography

Selected publications

• Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes

  Heredity · 2025-10-30 · 1 citations

  articleOpen access

  Phased genomes and pangenomes are enhancing our understanding of genetic variation. Accurate phasing and assembly in repetitive regions of the genome remain challenging, however. Addressing this obstacle is crucial for studying structural genomic variation, such as copy number variations (CNVs) common to repetitive regions. Polar fishes, for example, evolved repetitive tandem arrays of antifreeze protein (AFP) genes that facilitate adaptation to freezing and expanded in copy number in colder environments. AFP CNVs remain poorly characterized in polar fishes and may be illuminated by haplotype-aware approaches. We performed long-read sequencing for two polar fishes in the suborder Zoarcoidei and leveraged additional published long-read data to assemble phased genomes. We developed a workflow to measure haplotype diversity in CNV while controlling for misassembly and switch errors-a change from one parental haplotype to another in a contiguous assembly. We present gfa_parser, which computes and extracts all possible contiguous sequences for phased or primary assemblies from graphical fragment assembly (GFA) files, and switch_error_screen, which flags potential switch errors. gfa_parser revealed that assembly uncertainty was ubiquitous across AFP array haplotypes and that standard processing of graphical fragment assemblies can bias measurement of haplotype CNVs. We detected no switch errors in AFP arrays. After controlling for misassembly and switch error, we detected haplotype diversity of AFP CNVs in all studied polar Zoarcoidei species and in 60% of AFP arrays. Intraindividual haplotype diversity spanned differences of 3-16 copies. Our workflow revealed intraspecific genomic diversity in zoarcoids that likely fueled the evolution of AFP copy number across temperature.

  PublisherOA PDFDOI

• Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species

  Zenodo (CERN European Organization for Nuclear Research) · 2025-10-29

  datasetOpen access

  These are the files generated for the manuscript: T. B. Wooldridge, M. Escalona, B. W. Perry, A. N. Enstrom, D. Salih, W. E. Seligmann, S. Sacco, K. L. Moon, R. Sahasrabudhe, N. Chumchim, O. Nguyen, J. L. Kelley, R. D. E. MacPhee, B. Shapiro, Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species. Genome Biol. Evol., evaf188 (2025). DOI: 10.1093/gbe/evaf188 This is a complementary resource for the manuscript. Additional code corresponding to the analyses in the manuscript can be found here: https://github.com/twooldridge/BearComparativeGenomics AssembliesThe genome assemblies have been submitted to NCBI and should be available soon. The sequences are named: SCAF_X, where X is a number, and they are ordered based on sequence length. For the assemblies tagged as chromosome-level assemblies, we are sharing a table that specifies the relationship between the names. Please follow the prefix of the assemblies to get the CSV file corresponding to the chromosome-assignment table. Files shared: Assemblies: mHalMal1.NCBI.p_ctg.fasta.gz mHalMal1.NCBI.a_ctg.fasta.gz mTreOrn2.NCBI.p_ctg.fasta.gz mTreOrn2.NCBI.a_ctg.fasta.gz mMelUrs1.NCBI.p_ctg.fasta.gz mMelUrs1.NCBI.a_ctg.fasta.gz Chromosome-assignment: mHelMal1.NCBI.p_ctg.chrs.csv mMelUrs1.NCBI.p_ctg.chrs.csv mTreOrn2.NCBI.p_ctg.chrs.csv More information about the assemblies shared: Helarctos malayanus: BioSample: SAMN49720842 Assemblies: mHalMal1.NCBI.p_ctg.fasta.gz: Primary haplotype assembly. Chromosome-level. PRJNA1284979 : Helarctos malayanus Genome sequencing primary haplotype (TaxID: 9634) Locus Tag Prefixes: ACSF8I WGS Accession: JBREYN000000000 mHalMal1.NCBI.a_ctg.fasta.gz: Alternate haplotype assembly. Scaffold-level. PRJNA1284979 : Helarctos malayanus Genome sequencing alternate haplotype (TaxID: 9634) Locus Tag Prefixes: ACSF8J WGS Accession: JBREYO000000000 Tremartctos onrnatus: BioSample: SAMN49720843 Assemblies: mTreOrn2.NCBI.p_ctg.fasta.gz: Primary haplotype assembly. Chromosome-level. PRJNA1284975 : Tremarctos ornatus Genome sequencing (TaxID: 9638) Assembly Accession GCA_054642835.1 Locus Tag Prefixes: ACSF8H WGS Accession: JBTVSB000000000 mTreOrn2.NCBI.a_ctg.fasta.gz: Alternate haplotype assembly. Scaffold-level. PRJNA1284974 : Tremarctos ornatus Genome sequencing (TaxID: 9638) Assembly Accession GCA_054642835.1 Locus Tag Prefixes: ACSF8G WGS Accession: JBTVSC000000000 Melursus ursinus: BioSample: SAMN49720841 Assemblies: mMelUrs1.NCBI.p_ctg.fasta.gz: Primary haplotype assembly. Chromosome-level. PRJNA1284966 : Melursus ursinus Genome sequencing principal haplotype (TaxID: 9636) Locus Tag Prefixes: ACSF8E WGS Accession: JBQCBQ000000000 mMelUrs1.NCBI.a_ctg.fasta.gz: Alternate haplotype assembly. Scaffold-level. PRJNA1284968 : Melursus ursinus Genome sequencing alternate haplotype (TaxID: 9636) Locus Tag Prefixes: ACSF8F WGS Accession: JBQCBR000000000 Annotations Please note that these annotations were used for the analyses in our manuscript. Genes For each of the Brown, Black, Asiatic Black, Polar, Giant Panda, Sun, Sloth, and Andean bears, the following EGAPx genome annotation files are provided. See publication for details of EGAPx methods Files: ${SPECIES}.egapx.genomic.gff.gz - GFF formatted output from EGAPx (gzipped) ${SPECIES}.egapx.genomic.gtf.gz - GTF formatted output from EGAPx (gzipped) ${SPECIES}.egapx.cds.fna.gz - fasta file of coding sequences annotated with EGAPx (gzipped) ${SPECIES}.egapx.proteins.faa.gz - fasta file of protein sequences annotated with EGAPx (gzipped) ${SPECIES}.egapx.transcripts.fna.gz - fasta file of transcripts sequences annotated with EGAPx (gzipped) Repeats For each of the Brown, Black, Asiatic Black, Polar, Giant Panda, Sun, Sloth, and Andean bears, the following RepeatMasker files are provided. See the publication for the details of RepeatModeling + RepeatMasking methods. Files: ${SPECIES}.fasta.out.gff.gz - GFF-formatted output from RepeatMasker (gzipped) ${SPECIES}.fasta.out.html - HTML Repeat Masker report ${SPECIES}.fasta.tbl - Repeat Masker summary table ${SPECIES}.fasta.masked.gz- Soft-masked (A->a) reference genome (gzipped)

  PublisherDOI

• Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes

  Molecular Biology and Evolution · 2025-09-11 · 2 citations

  articleOpen accessSenior author

  Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes' tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

  PublisherDOI

• Drivers of genetic diversity across the marine tree of life

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-06 · 2 citations

  preprintOpen access

  Why do some species have more genetic diversity than others? This question is one of the greatest remaining mysteries in evolutionary biology, and is particularly urgent in marine species, which are experiencing catastrophic anthropogenic impacts. We address this critical gap by estimating genetic diversity for 93 marine species sampled over 9,000 localities. For each species, we aggregate biotic traits and abiotic geographic data for their ranges. We show that diversity increases with range extent and planktonic dispersal. We hypothesize that these traits increase a species' ability to avoid or recover from bottlenecks, thereby maintaining diversity. Our findings provide insights into the factors interacting to shape genomic variation in the ocean, and offer a predictive framework for understanding marine biodiversity in the face of global change.

  PublisherOA PDFDOI

• Bridging the gap between legacy polymerase chain reaction-based microsatellite data with high-throughput sequencing data for conservation genomics

  Journal of Heredity · 2025-11-01

  articleOpen accessSenior author

  Microsatellites are powerful markers for tracking genetic variation in wildlife populations due to their high polymorphism and genome-wide abundance. While PCR-based fragment size analysis has been the standard for genotyping microsatellites, high-throughput sequencing offers greater resolution and the opportunity to sync historical datasets with modern analyses. We evaluated how genotypes from whole-genome sequencing align with PCR data for 15 microsatellite loci in 11 North American brown bears (Ursus arctos). Brown bear populations in the lower 48 United States have declined from approximately 50,000 to fewer than 2,000 over the past decades. Their endangered status has prompted extensive research and genetic monitoring, yielding large, multi-year microsatellite datasets upon which future conservation efforts can build. We achieved a microsatellite genotype concordance rate of 94.5% with PCR results. All discrepancies occurred at complex loci containing multiple insertions and/or deletions (indels). Physically linked indels or single nucleotide polymorphisms (SNPs) occurring within the loci were misinterpreted as independent insertions, underscoring the need for genotyping tools that incorporate phasing when genotyping. To evaluate coverage effects, we downsampled from 30x to 2x. Concordance remained high at 20-30x but dropped sharply at 10x, with 5x and 2x having discordant genotypes or insufficient coverage for genotyping. Accurate genotyping required both sufficient depth and number of reads spanning the entire repeat regions. Our results show that short-read whole-genome sequencing can recover microsatellite genotypes with high accuracy when paired with careful variant interpretation. By aligning historical PCR datasets with modern sequencing data, we can preserve decades of genetic insight and strengthen long-term monitoring of at-risk populations.

  PublisherDOI

• Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics

  Genome Biology and Evolution · 2025-01-21 · 8 citations

  articleOpen access

  Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil taxa. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo and post mortem. This raises the question as to whether the enamelome alone provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments for each protein and estimated the evolutionary rate for each site. We examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1 to 2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We tested phylogenetic analysis on combinations of different enamel proteins and found that the composition of the proteome can influence deep splits in the phylogeny. With our methods, we provide guidance for researchers on how to evaluate the potential of paleoproteomics for phylogenetic studies before sampling valuable ancient specimens.

  PublisherOA PDFDOI

• Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-15

  preprintOpen access

  Phased genomes and pangenomes are enhancing our understanding of genetic variation. Accurate phasing and assembly in repetitive regions of the genome remain challenging, however. Addressing this obstacle is crucial for studying structural genomic variation such as copy number variations (CNVs) common to repetitive regions. Polar fishes, for example, evolved repetitive tandem arrays of antifreeze protein (AFP) genes that facilitated adaptation to freezing and expanded in copy number in colder environments. AFP CNVs remain poorly characterized in polar fishes and may be illuminated by haplotype-aware approaches. We performed long-read sequencing of two polar fishes in the suborder Zoarcoidei and leveraged published long-read data to assemble phased genomes. We developed a workflow to measure haplotype diversity in CNV while controlling for misassembly and switch errors - a change from one parental haplotype to another in a contiguous assembly. We present gfa_parser , which computes and extracts all possible contiguous sequences for phased or primary assemblies from graphical fragment assembly files, and switch_error_screen , which flags potential switch errors. gfa_parser revealed that assembly uncertainty was ubiquitous across AFP array haplotypes and that standard processing of graphical fragment assemblies can bias measurement of haplotype CNVs. We detected no switch errors in AFP arrays. After controlling for misassembly and switch error, we detected haplotype diversity of AFP CNVs in all studied polar Zoarcoidei species and in 60% of AFP arrays. Intraindividual haplotype diversity spanned differences of 3-16 copies. Our workflow revealed intraspecific genomic diversity in zoarcoids that likely fueled evolution of AFP copy number across temperature.

  PublisherOA PDFDOI

• Embryonic thermal environments drive plasticity in gene expression

  Fish Physiology and Biochemistry · 2025-06-01 · 3 citations

  articleOpen accessSenior author

  When embryos experience different environments than their parents, plasticity can enable the development of alternate phenotypes that confer higher fitness in the new conditions. Temperature-induced plasticity could be especially critical for species that inhabit areas with considerable thermal variation. We studied transcriptional variation in embryos of mangrove rivulus (Kryptolebias marmoratus)-a self-fertilizing hermaphroditic, eurythermal fish that resides in notoriously spatiotemporally variable mangrove forests-exposed to different thermal regimes during development. To study transcriptional plasticity, we first improved the genome assembly to chromosome length scaffolds (N50 of 28.17 Megabases). Whole transcriptome sequencing revealed that both temperature and developmental timing modulated embryonic gene expression. We found few differences in gene expression between embryos incubated in cold and warm conditions and assessed before the temperature-sensitive period of development, indicating high resistance to stochastic changes in gene expression early in development. Replicate embryos exposed to cold temperatures and sampled after the temperature-sensitive period showed less variation in gene expression than those sampled before, suggesting canalization of the plastic response. DNA replication/repair, organelle, and gas transport pathways were upregulated while nervous system development, cell signaling, and cell adhesion were downregulated in cold-exposed compared to warm-exposed embryos sampled after the temperature-sensitive period. These plastic shifts in gene expression could have major implications for reorganizing the phenotype (e.g., apoptosis, mitosis) in response to environmental changes occurring within a generation.

  PublisherOA PDFDOI

• Genomic Insights into Bear Hibernation

  Annual Review of Genetics · 2025-07-04 · 1 citations

  reviewOpen accessSenior author

  Hibernation is a fascinating adaptation to food-scarce winters, characterized by significant physiological and behavioral changes, including fasting, inactivity, and insulin resistance. While hibernation is critical for the survival of many species, hibernation-related traits are often considered pathological in humans. Hibernation has been studied from a genomic perspective, especially with respect to transcription across multiple tissues. These studies have identified the differential activity of signaling pathways related to metabolism, tissue protection, and other mechanisms likely underlying hibernation phenotypes. Bears, in particular, are an interesting model for physiological and genomic studies of hibernation due to their large size and unique mode of hibernation compared to other small mammalian hibernators. Investigating the intricate molecular mechanisms underlying bear hibernation may therefore provide insight into fundamental biological processes with potential translational implications for human health, particularly with respect to metabolic disorders such as type II diabetes. This review focuses on recent advances and outstanding questions related to the exploration of bear hibernation from a genomic perspective.

  PublisherDOI

• New Genome Assemblies for Poeciliidae: A Foundation for Adaptation Studies

  Genome Biology and Evolution · 2025-05-30

  articleOpen accessSenior author

  Multiple lineages in the family Poeciliidae have independently adapted to hydrogen-sulfide-rich springs. The independent colonizations of such springs mean that there are naturally replicated lineages that provide a powerful model for studying adaptation and convergent evolution. However, there are limited genomic resources for many genera and species across Poeciliidae. Here, we present six high-quality, chromosome-level, annotated genome assemblies for Poecilia and Gambusia populations, five of which are the first for the species or ecotype, and the remaining assembly improved the current reference genome contiguity by more than 100-fold. Using these new assemblies, we compare repeat content and model historical changes in effective population size.

  PublisherOA PDFDOI

Recent grants

• NIH Grant F32GM087069

  NIH · $99k · 2012

• Genome Evolution in Polar Fishes

  NSF · $831k · 2019–2023

• COLLABORATIVE RESEARCH: Physiological Adaptation to Extreme Environments: Genes, Function, and Evolutionary Patterns

  NSF · $305k · 2016–2021

• ROL: COLLABORATIVE RESEARCH: EXTREME ENVIRONMENTS, PHYSIOLOGICAL ADAPTATION, AND THE ORIGIN OF SPECIES

  NSF · $547k · 2023–2025

• ROL: COLLABORATIVE RESEARCH: EXTREME ENVIRONMENTS, PHYSIOLOGICAL ADAPTATION, AND THE ORIGIN OF SPECIES

  NSF · $604k · 2020–2023

Frequent coauthors

• Michael Tobler

  Saint Louis Zoo

  54 shared

• Lenin Arias‐Rodríguez

  Universidad Juárez Autónoma de Tabasco

  40 shared

• Tomás Marquès‐Bonet

  Universitat Autònoma de Barcelona

  38 shared

• Carlos D. Bustamante

  34 shared

• Scott Hotaling

  32 shared

• Ryan Greenway

  Kansas State University

  25 shared

• Kerry L. McGowan

  25 shared

• Paul B. Frandsen

  Brigham Young University

  23 shared