About

Dr. Ian Wang is an Associate Professor of Quantitative Landscape Ecology in the Department of Environmental Science, Policy, and Management at UC Berkeley, with an affiliation in the Museum of Vertebrate Zoology. His research explores how environmental variation influences genetic, phenotypic, and ecological diversity across different spatial and temporal scales. Combining methods such as landscape genomics, remote sensing, and morphological evolution, his lab investigates the mechanisms that generate biodiversity and how species respond to environmental change. His work has revealed insights into how genomic architecture affects adaptive potential, the role of seasonal asynchrony and ecological divergence as barriers to gene flow, and the contribution of hybridization and transgressive evolution to adaptive radiation. Additionally, his group develops tools for spatial genomic analysis and leads applied conservation genomics efforts, including collaborations with the California Conservation Genomics Project.

Research topics

• Biology
• Social Science
• Computer Science
• Ecology
• Sociology
• Data science
• Engineering
• Genetics
• Geography
• Environmental resource management
• Paleontology
• Engineering ethics

Selected publications

• Diagnostic performance of transcutaneous laryngeal ultrasound for vocal cord paralysis after esophagectomy: a systematic review and meta-analysis

  Esophagus · 2025-10-24

  review
  PublisherDOI

• Abstract B047: Discovery of a covalent inhibitor targeting PAX8-driven ovarian cancer

  Molecular Cancer Therapeutics · 2025-10-22

  article

  Abstract The paired box (PAX) family of transcription factors plays critical roles in embryonic development but is largely silenced in most adult tissues. Among them, PAX8 has emerged as a lineage-specific oncogenic driver in uterine and ovarian cancers – tumor types characterized by high incidence, limited therapeutic options, and poor clinical outcomes. Genetic knockout and knockdown studies have consistently demonstrated strong anti-tumor activity across diverse ovarian cancer cell lines, firmly establishing PAX8 as a as a critical dependency in these malignancies. As a lineage-restricted transcription factor, PAX8 regulates the expression of critical oncogenes such as FGF18 and CCNA2, and its elevated activity correlates with poor patient prognosis, highlighting its potential as a compelling therapeutic target with a favorable safety profile due to its limited expression in normal adult tissues. Despite its therapeutic potential, PAX8 has long been considered “undruggable” due to the absence of well-defined small-molecule binding pockets and its dependence on DNA binding for function. To overcome this challenge, we applied BridGene’s proprietary IMTAC™ (Isobaric Mass Tagged Affinity Characterization) platform and identified PAX8 covalent binders targeting PAX8 in live cell screening. This approach led to the discovery of a hit compound, which was further optimized through structure–activity relationship (SAR) studies to yield BGP-31609 with enhanced potency, selectivity, and drug-like properties. BGP-31609 irreversibly binds to a single, functionally critical cysteine residue within the DNA-binding domain of PAX8, thereby providing a novel, targeted mechanism of action against this historically undruggable transcription factor. In a series of biochemical and cellular assays, BGP-31609 demonstrated robust on-target activity with minimal off-target concern. It showed dose-responsive inhibition of DNA binding in Electrophoretic mobility shift assay (EMSA), and inhibited PAX8 driven transcription activity in TPO-luciferase reporter assay, while has minimum effects in ERK driven SRE-luciferase reporter assay. In viability assays, it selectively reduced growth of PAX8-high OVCAR3 cells, while showing no effect on PAX8-negative A549 cells. Gene expression analysis by qPCR revealed suppression of PAX8 target genes in OVCAR3 cells. Together, these findings establish BGP-31609 as a mechanistically validated hit compound that covalently binds PAX8 at a single site and impairs its transcriptional function and tumor cell proliferation. BridGene is actively advancing BGP-31609 to further enhance its potency, selectivity, and druggability, aiming for a novel therapy for PAX8-dependent cancers. Citation Format: Yining Hao, Steve Luo, Maryam Quraishi, Ian Wang, Vivian Zhang, Monica M. Kangussu-Marcolino, Rajani Ravishankar, Iris Dong, Jingyu Dong, Anna Chen, Ning Deng, Ping Cao, Shirley Guo. Discovery of a covalent inhibitor targeting PAX8-driven ovarian cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr B047.

  PublisherDOI

• A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-17

  preprint

  We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

  PublisherDOI

• Genome resources—A chromosome-level genome assembly for the long-nosed leopard lizard, <i>Gambelia wislizenii</i> , the first reference genome for the lizard family Crotaphytidae

  Journal of Heredity · 2025-07-30

  articleOpen access

  We report on an annotated chromosome-level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, as part of the California Conservation Genomics Project (CCGP). All 17 species of reptiles, including two turtles, seven lizards, and seven snakes targeted for reference genome sequencing by the CCGP are now complete and posted on NCBI, and this article is the third of seven CCGP lizard release papers to be published. It is also the first species of the family Crotaphytidae to have a released reference genome. Following the CCGP pipeline, the G. wislizenii genome was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. The de novo assembly includes 69 scaffolds and has a total length of ~ 2.47 Gb, a scaffold N50 length of 380.1 Mb, and a BUSCO completeness score of 97.4% based on the tetrapod gene set. We improved the annotation of the genome using transcriptome sequencing (seven tissue types), identifying 23,279 genes, with BUSCO completeness of 98.9%. This reference genome, when combined with CCGP's on-going state-wide resequencing efforts for the three species of Gambelia in California, including the federally endangered blunt-nosed leopard lizard (Gambelia sila), and Cope's leopard lizard (Gambelia copei), will be a powerful tool enabling researchers to characterize hybridization dynamics between Gambelia species, document the remaining diversity within G. sila, and explore the genetic underpinnings of key traits that vary between the three Gambelia species, such as territoriality, sexual size dimorphism, presence versus absence of male breeding coloration, and skull morphologies.

  PublisherOA PDFDOI

• Reference genome of the Gophersnake, <i>Pituophis catenifer</i> (Serpentes: Colubridae)

  Journal of Heredity · 2025-04-10

  article

  The Gophersnake, Pituophis catenifer, is a habitat generalist that ranges throughout the western half of the United States and southward into México. Five of the six subspecies, P. catenifer affinis (Sonoran Gophersnake), P. catenifer annectens (San Diego Gophersnake), P. catenifer catenifer (Pacific Gophersnake), P. catenifer deserticola (Great Basin Gophersanke), and P. catenifer pumilus (Santa Cruz Island Gophersnake), occur in California and span virtually all the state's diverse terrestrial habitats. These subspecies are ecologically and morphologically distinct from one another, although existing genetic data indicate there is genetic admixture across some of their contact zones. Given that these subspecies occur in such different environments they will not all respond to climate change and anthropogenic stressors equally. Here, we report a new, chromosome-level assembly of P. catenifer as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 426 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.5 Mb, a scaffold N50 of 161 Mb, and BUSCO completeness score of 95.3%. This genome will be a foundational resource for future studies on the conservation, adaptation, biogeography, and systematics of P. catenifer.

  PublisherDOI

• Loss of pigments in females is associated with sexual dichromatism in an ornamental trait

  Evolution · 2025-04-07 · 2 citations

  articleOpen access

  Sexual dichromatism is thought to evolve primarily as a function of sexual selection, especially female choice. However, other forces, from sex-specific environmental conditions to social signaling in females, can also generate color differences between sexes. We studied dewlap dichromatism across 292 species of Anolis lizards. Dewlaps are colorful throat ornaments found on males of most anole species but are also present in females in many species. Although male and female dewlaps often have similar coloration, in some species, they are strikingly dichromatic. We found that ornament color is labile and that dichromatism results from the loss of costly pigments in females. This pattern could indicate a shift towards signal loss in females; however, the secondary gains of female dewlaps across the phylogeny suggest a potential advantageous function. Possible mechanisms for female dewlap coloration include social selection, nonsexual signaling, or detectability in different microhabitats (e.g., sensory drive). Female dewlap color overlap between co-occurring species is both less than expected by chance overall and reduced in species-rich communities, suggesting that dichromatism could be driven by competition. Our results highlight that selection on females drives the observed pattern of dichromatism, suggesting a potentially adaptive role for female ornaments and emphasizing the need for additional work to understand female ornament evolution.

  PublisherDOI

• A chromosome-level reference genome assembly for Gilbert’s skink <i>Plestiodon gilberti</i>

  Journal of Heredity · 2025-06-21 · 1 citations

  articleOpen access

  Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert's skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project. This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. Although members of the Scincidae comprise nearly one-quarter of all lizard species (1785 described species), this de novo assembly represents one of only 10 skink species globally and the first North American skink with a reference genome. The assembly has a total length of ~ 1.57 Gb, a scaffold N50 length of ~ 231.32 Mb, read coverage of ~56X, and BUSCO completeness score of 97.2% based on the Tetrapoda ortholog database. Plestiodon gilberti is a member of the Plestiodon skiltonianus species complex, a group with many of the characteristics of ecological speciation but where ancient hybridization and biased introgression present challenges to retracing the initial patterns of lineage divergence. Combined with dense sampling of resequenced genomes in the California Conservation Genomics Project, including other members of the P. skiltonianus complex, this reference genome will enable future analyses of the links between divergent selection and the genes underlying speciation, as well as the potential for introgression to enable adaptation to new or changing environments.

  PublisherOA PDFDOI

• Global phenology maps reveal the drivers and effects of seasonal asynchrony

  Nature · 2025-08-27 · 14 citations

  articleOpen accessSenior author

  Abstract Terrestrial plant communities show great variation in their annual rhythms of growth, or seasonal phenology 1,2 . The geographical patterns resulting from this variation, known as land surface phenology (LSP) 3 , contain valuable information for the study of ecosystem function 4,5 , plant ecophysiology 6–8 , landscape ecology 9,10 and evolutionary biogeography 11–13 . Yet globally consistent LSP mapping has been hampered by methods that struggle to represent the full range of seasonal phenologies occurring across terrestrial biomes 14 , especially the subtle and complex phenologies of many arid and tropical ecosystems 1,15,16 . Here, using a data-driven analysis of satellite imagery to map LSP worldwide, we provide insights into Earth’s phenological diversity, documenting both intercontinental convergence between similar climates and regional heterogeneity associated with topoclimate, ecohydrology and vegetation structure. We then map spatial phenological asynchrony and the modes of asynchronous seasonality that control it, identifying hotspots of asynchrony in tropical mountains and Mediterranean climate regions and reporting evidence for the hypothesis that climatically similar sites exhibit greater phenological asynchrony within the tropics. Finally, we find that our global LSP map predicts complex geographical discontinuities in flowering phenology, genetic divergence and even harvest seasonality across a range of taxa, establishing remote sensing as a crucial tool for understanding the ecological and evolutionary consequences of allochrony by allopatry.

  PublisherOA PDFDOI

• Throat Color Polymorphism is Related to Differences in Aggression in Aegean Wall Lizards

  Herpetologica · 2025-01-10

  article

  Aggressive behavior can be used to establish and maintain access to crucial resources such as space, food, and mating opportunities. Color polymorphic animals sometimes exhibit morph-correlated aggressive behaviors that can influence relative reproductive success and, thus, the maintenance of polymorphism. Aegean wall lizards, Podarcis erhardii, exhibit one of three monochromatic throat color morphs: orange, white, and yellow. Previously, male P. erhardii color morphs were shown to differ in their use of aggressive behaviors and ability to win staged contests during laboratory experiments. However, whether these color morphs use aggressive behavior differently in their natural setting where ecological and environmental factors are not standardized remains unknown. Here, we observed interactions of wall lizards over a large section of dry stone wall to investigate behavioral differences in aggression among color morphs in situ. We compared the counts and intensities (aggression scores) of aggressive behaviors (both performing and receiving aggression) and found that color morphs differ significantly in the frequencies and intensities of their aggressive behaviors. White morphs exhibited significantly more aggression than orange and yellow morphs on dry stone walls. Taken together, results from in situ and ex situ behavioral studies suggest that the smaller, more common white color morphs are more aggressive, which may help explain their relatively greater abundance and persistence across the species' range.

  PublisherDOI

• Anti-predator defences are linked with high levels of genetic differentiation in frogs

  Proceedings of the Royal Society B Biological Sciences · 2024-01-24 · 6 citations

  articleOpen access

  Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.

  PublisherOA PDFDOI

Recent grants

• Dimensions: Landscape Genomics of an Adaptive Radiation using Ultra-High Resolution Genetic, Morphometric, and Spatial Analysis

  NSF · $1.5M · 2016–2022

• CAREER: Understanding Evolutionary Responses to Climate Change Across Space and Time

  NSF · $899k · 2019–2025

Frequent coauthors

• Michael L. Yuan

  California Academy of Sciences

  41 shared

• H. Bradley Shaffer

  California Department of Conservation

  35 shared

• Erin Toffelmier

  California Department of Conservation

  28 shared

• Jonathan B. Losos

  Washington University in St. Louis

  27 shared

• Chuan‐Yu Chen

  National Health Research Institutes

  25 shared

• Erin P. Westeen

  University of Michigan–Ann Arbor

  21 shared

• Merly Escalona

  University of California, Santa Cruz

  20 shared

• Eric Beraut

  University of California, Santa Cruz

  18 shared

Education

• Ph.D., Center for Population Biology

  University of California Davis

  2010

• B.A., Ecology and Evolutionary Biology

  Cornell University

  2004

Awards & honors

• Jasper Loftus-Hills Young Investigator's Award from the Amer…
• NSF Career Award (2019)
• UC Berkeley Faculty Award for Excellence in Postdoctoral Men…
• Hellman Foundation Fellow (2016)